Frequency distribution of space groups in soluble and membrane proteins and their complexes
The space-group frequency distributions for two types of proteins and their complexes are explored. Based on the incremental availability of data in the Protein Data Bank, an analytical assessment shows a preferential distribution of three space groups, i.e. P212121> P1211> C121, in soluble and membrane proteins as well as in their complexes. In membrane proteins, the order of the three space groups is P212121> C121> P1211. The distribution of these space groups also shows the same pattern whether a protein crystallizes with a monomer or an oligomer in the asymmetric unit. The results also indicate that the siz...
Source: Acta Crystallographica Section F - June 7, 2021 Category: Biochemistry Authors: Gaur, R.K. Tags: protein crystallography space groups crystal systems frequency distribution research communications Source Type: research
Structure of a dimer of the Sulfolobus solfataricus MCM N-terminal domain reveals a potential role in MCM ring opening
Cells strongly regulate DNA replication to ensure genomic stability and prevent several diseases, including cancers. Eukaryotes and archaea strictly control DNA-replication initiation by the regulated loading of hexameric minichromosome maintenance (MCM) rings to encircle both strands of the DNA double helix followed by regulated activation of the loaded rings such that they then encircle one DNA strand while excluding the other. Both steps involve an open/closed ring transformation, allowing DNA strands to enter or exit. Here, the crystal structure of a dimer of the N-terminal domain of Sulfolobus solfataricus MCM with an...
Source: Acta Crystallographica Section F - June 1, 2021 Category: Biochemistry Authors: Meagher, M. Spence, M.N. Enemark, E.J. Tags: DNA replication helicases MCM minichromosome maintenance Sulfolobus solfataricus research communications Source Type: research
Crystal structures of two camelid nanobodies raised against GldL, a component of the type IX secretion system from Flavobacterium johnsoniae
GldL is an inner-membrane protein that is essential for the function of the type IX secretion system (T9SS) in Flavobacterium johnsoniae. The complex that it forms with GldM is supposed to act as a new rotary motor involved in the gliding motility of the bacterium. In the context of structural studies of GldL to gain information on the assembly and function of the T9SS, two camelid nanobodies were selected, produced and purified. Their interaction with the cytoplasmic domain of GldL was characterized and their crystal structures were solved. These nanobodies will be used as crystallization chaperones to help in the crystal...
Source: Acta Crystallographica Section F - May 24, 2021 Category: Biochemistry Authors: Trinh, T.T.N. Gaubert, A. Melani, P. Cambillau, C. Roussel, A. Leone, P. Tags: camelid nanobodies type IX secretion system Flavobacterium johnsoniae GldL interaction crystallization chaperones domain swapping research communications Source Type: research
Crystal structure of the Thr316Ala mutant of a yeast JAMM deubiquitinase: implication of active-site loop dynamics in catalysis
AMSH, an endosome-associated deubiquitinase (DUB) with a high specificity for Lys63-linked polyubiquitin chains, plays an important role in endosomal – lysosomal sorting and down-regulation of cell-surface receptors. AMSH belongs to the JAMM family of DUBs that contain two insertion segments, Ins-1 and Ins-2, in the catalytic domain relative to the JAMM core found in the archaebacterial AfJAMM. Structural analyses of the AMSH homologs human AMSH-LP and fission yeast Sst2 reveal a flap-like structure formed by Ins-2 near the active site that appears to open and close during its catalytic cycle. A conserved phenylalani...
Source: Acta Crystallographica Section F - May 24, 2021 Category: Biochemistry Authors: Shrestha, R. Das, C. Tags: deubiquitinating enzymes JAMM domains ESCRT complexes Lys63-linked polyubiquitin-chain deubiquitinase research communications Source Type: research
Crystal structure of enoyl-CoA hydratase from Thermus thermophilus HB8
Fatty-acid degradation is an oxidative process that involves four enzymatic steps and is referred to as the β -oxidation pathway. During this process, long-chain acyl-CoAs are broken down into acetyl-CoA, which enters the mitochondrial tricarboxylic acid (TCA) cycle, resulting in the production of energy in the form of ATP. Enoyl-CoA hydratase (ECH) catalyzes the second step of the β -oxidation pathway by the syn addition of water to the double bond between C2 and C3 of a 2-trans-enoyl-CoA, resulting in the formation of a 3-hydroxyacyl CoA. Here, the crystal structure of ECH from Thermus thermophilus HB8 (TtECH) ...
Source: Acta Crystallographica Section F - May 4, 2021 Category: Biochemistry Authors: Padavattan, S. Jos, S. Gogoi, H. Bagautdinov, B. Tags: β -oxidation pathway crotonases enoyl-CoA hydratase crystal structure fatty-acid metabolism Thermus thermophilus HB8 research communications Source Type: research
A new crystal form of GABARAPL2
This article reports a new, untwinned GABARAPL2 crystal form, also in space group P21, but with a 98 ° monoclinic angle. No major conformational differences were observed between the structures. In the structure described here, the C-terminal Phe117 binds into the LIR docking site (LDS) of a neighbouring molecule within the asymmetric unit, as observed in the previously reported structure. This crystal contact blocks the LDS for co-crystallization with ligands. Phe117 of GABARAPL2 is normally removed during biological processing by Atg4 family proteases. These data indicate that to establish interactions with the LIR, ...
Source: Acta Crystallographica Section F - April 30, 2021 Category: Biochemistry Authors: Scicluna, K. Dewson, G. Czabotar, P.E. Birkinshaw, R.W. Tags: GABARAPL2 GATE-16 Atg8 autophagy autophagosome LIR LC3 research communications Source Type: research
Crystallographic analysis and phasing of iron-assimilating protein 1 (FEA1) from Chlamydomonas reinhardtii
This study will lead to further structural studies of FEA1 to understand its function and its links to the iron-assimilation pathway. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 30, 2021 Category: Biochemistry Authors: Juniar, L. Adlfar, V. Hippler, M. Tanaka, H. Kurisu, G. Tags: iron transport FEA1 SAD Chlamydomonas reinhardtii research communications Source Type: research
Simplified heavy-atom derivatization of protein structures via co-crystallization with the MAD tetragon tetrabromoterephthalic acid
The phase problem is a persistent bottleneck that impedes the structure-determination pipeline and must be solved to obtain atomic resolution crystal structures of macromolecules. Although molecular replacement has become the predominant method of solving the phase problem, many scenarios still exist in which experimental phasing is needed. Here, a proof-of-concept study is presented that shows the efficacy of using tetrabromoterephthalic acid (B4C) as an experimental phasing compound. Incorporating B4C into the crystal lattice using co-crystallization, the crystal structure of hen egg-white lysozyme was solved using MAD p...
Source: Acta Crystallographica Section F - April 28, 2021 Category: Biochemistry Authors: Truong, J.Q. Nguyen, S. Bruning, J.B. Shearwin, K.E. Tags: crystallography experimental phasing B4C tetrabromoterephthalic acid lysozyme co-crystallization research communications Source Type: research
Engineering and crystal structure of a monomeric FLT3 ligand variant
The overarching paradigm for the activation of class III and V receptor tyrosine kinases (RTKs) prescribes cytokine-mediated dimerization of the receptor ectodomains and homotypic receptor – receptor interactions. However, structural studies have shown that the hematopoietic receptor FLT3, a class III RTK, does not appear to engage in such receptor – receptor contacts, despite its efficient dimerization by dimeric FLT3 ligand (FL). As part of efforts to better understand the intricacies of FLT3 activation, we sought to engineer a monomeric FL. It was found that a Leu27Asp substitution at the dimer interface of ...
Source: Acta Crystallographica Section F - April 6, 2021 Category: Biochemistry Authors: Pannecoucke, E. Raes, L. Savvides, S.N. Tags: FLT3 ligand receptor tyrosine kinases acute myeloid leukemia research communications Source Type: research
Crystal structure of hemoglobin from mouse (Mus musculus) compared with those from other small animals and humans
Mice (Mus musculus) are nocturnal small animals belonging to the rodent family that live in burrows, an environment in which significantly high CO2 levels prevail. It is expected that mouse hemoglobin (Hb) plays an important role in their adaptation to living in such a high-CO2 environment, while many other species cannot. In the present study, mouse Hb was purified and crystallized at a physiological pH of 7 in the orthorhombic space group P212121; the crystals diffracted to 2.8 Å resolution. The primary amino-acid sequence and crystal structure of mouse Hb were compared with those of mammalian Hbs in order to i...
Source: Acta Crystallographica Section F - April 1, 2021 Category: Biochemistry Authors: Sundaresan, S.S. Ramesh, P. Shobana, N. Vinuchakkaravarthy, T. Yasien, S. Ponnuswamy, M.N.G. Tags: hemoglobin mouse oxygen transport oxygen storage methemoglobin research communications Source Type: research
Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions
Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper – oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallography provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crys...
Source: Acta Crystallographica Section F - March 31, 2021 Category: Biochemistry Authors: Schr ö der, G.C. O'Dell, W.B. Swartz, P.D. Meilleur, F. Tags: lytic polysaccharide monooxygenases Neurospora crassa neutron protein crystallography reduction protonation enzymatic mechanism methods communications Source Type: research
Crystal structure of the GTP-binding protein-like domain of AGAP1
AGAP1 is often considered to regulate membrane trafficking, protein transport and actin cytoskeleton dynamics. Recent studies have shown that aberrant expression of AGAP1 is associated with many diseases, including neurodevelopmental disorders and acute lymphoblastic leukemia. It has been proposed that the GTP-binding protein-like domain (GLD) is involved in the binding of cofactors and thus regulates the catalytic activity of AGAP1. To obtain a better understanding of the pathogenic mechanism underpinning AGAP1-related diseases, it is essential to obtain structural information. Here, the GLD (residues 70 – 235) of A...
Source: Acta Crystallographica Section F - March 31, 2021 Category: Biochemistry Authors: Cheng, N. Zhang, H. Zhang, S. Ma, X. Meng, G. Tags: AGAP1 GTP-binding protein-like domain X-ray crystallography research communications Source Type: research
Novel clostridial cell-surface hemicellulose-binding CBM3 proteins
A novel member of the family 3 carbohydrate-binding modules (CBM3s) is encoded by a gene (Cthe_0271) in Clostridium thermocellum which is the most highly expressed gene in the bacterium during its growth on several types of biomass substrates. Surprisingly, CtCBM3-0271 binds to at least two different types of xylan, instead of the common binding of CBM3s to cellulosic substrates. CtCBM3-0271 was crystallized and its three-dimensional structure was solved and refined to a resolution of 1.8 Å . In order to learn more about the role of this type of CBM3, a comparative study with its orthologue from Clostridium clari...
Source: Acta Crystallographica Section F - March 31, 2021 Category: Biochemistry Authors: Hershko Rimon, A. Livnah, O. Rozman Grinberg, I. Ortiz de Ora, L. Yaniv, O. Lamed, R. Bayer, E.A. Frolow, F. Voronov-Goldman, M. Tags: cellulosome CBM calcium binding crystal structure Clostridium thermocellum Clostridium clariflavum research communications Source Type: research
Crystal structure of the nonclassical cadherin-17 N-terminus and implications for its adhesive binding mechanism
The cadherin superfamily of calcium-dependent cell-adhesion proteins has over 100 members in the human genome. All members of the superfamily feature at least a pair of extracellular cadherin (EC) repeats with calcium-binding sites in the EC linker region. The EC repeats across family members form distinct complexes that mediate cellular adhesion. For instance, classical cadherins (five EC repeats) strand-swap their N-termini and exchange tryptophan residues in EC1, while the clustered protocadherins (six EC repeats) use an extended antiparallel `forearm handshake' involving repeats EC1 – EC4. The 7D-cadherins, cadhe...
Source: Acta Crystallographica Section F - March 4, 2021 Category: Biochemistry Authors: Gray, M.E. Sotomayor, M. Tags: cadherin-17 cell adhesion calcium binding intestinal epithelia LI-cadherin research communications Source Type: research
Structural analysis of the Sulfolobus solfataricus TF55 β chaperonin by cryo-electron microscopy
Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α , β and γ subunits. Using cryo-electron microscopy, structures of the β -only complex of S. solfataricus TF55 (TF55 β ) were determined to 3.6 – 4.2 Å resolution. The structures of the TF55 β complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 3, 2021 Category: Biochemistry Authors: Zeng, Y.C. Sobti, M. Stewart, A.G. Tags: chaperonins cryo-electron microscopy research communications Source Type: research
Crystal structure of human CRM1, covalently modified by 2-mercaptoethanol on Cys528, in complex with RanGTP
This study presents the crystal structure of human CRM1, covalently modified by 2-mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine-dependent inhibitor compounds. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 3, 2021 Category: Biochemistry Authors: Shaikhqasem, A. Schmitt, K. Valerius, O. Ficner, R. Tags: nuclear export cancer exportin 1 cysteine modification research communications Source Type: research
Crystal structures of anthranilate phosphoribosyltransferase from Saccharomyces cerevisiae
Anthranilate phosphoribosyltransferase (AnPRT) catalyzes the transfer of the phosphoribosyl group of 5 ′ -phosphoribosyl-1 ′ -pyrophosphate (PRPP) to anthranilate to form phosphoribosyl-anthranilate. Crystal structures of AnPRTs from bacteria and archaea have previously been determined; however, the structure of Saccharomyces cerevisiae AnPRT (ScAnPRT) still remains unsolved. Here, crystal structures of ScAnPRT in the apo form as well as in complex with its substrate PRPP and the substrate analogue 4-fluoroanthranilate (4FA) are presented. These structures demonstrate that ScAnPRT exhibits the conserved structu...
Source: Acta Crystallographica Section F - March 1, 2021 Category: Biochemistry Authors: Wu, X. Zhang, M. Kuang, Z. Yue, J. Xue, L. Zhu, M. Zhu, Z. Khan, M.H. Niu, L. Tags: anthranilate phosphoribosyltransferase Saccharomyces cerevisiae substrate binding crystal structure research communications Source Type: research
Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis
Rickettsia felis, a Gram-negative bacterium that causes spotted fever, is of increasing interest as an emerging human pathogen. R. felis and several other Rickettsia strains are classed as National Institute of Allergy and Infectious Diseases priority pathogens. In recent years, R. felis has been shown to be adaptable to a wide range of hosts, and many fevers of unknown origin are now being attributed to this infectious agent. Here, the structure of acetoacetyl-CoA reductase from R. felis is reported at a resolution of 2.0 Å . While R. felis acetoacetyl-CoA reductase shares less than 50% sequence identity with it...
Source: Acta Crystallographica Section F - February 16, 2021 Category: Biochemistry Authors: Rodarte, J.V. Abendroth, J. Edwards, T.E. Lorimer, D.D. Staker, B.L. Zhang, S. Myler, P.J. McLaughlin, K.J. Tags: SSGCID structural genomics Seattle Structural Genomics Center for Infectious Disease oxidoreductase Rickettsia acetoacetyl-CoA reductase PhaB research communications Source Type: research
Structural insights into the intermolecular interaction of the adhesin SdrC in the pathogenicity of Staphylococcus aureus
Staphylococcus aureus is an opportunistic disease-causing pathogen that is widely found in the community and on medical equipment. A series of virulence factors secreted by S. aureus can trigger severe diseases such as sepsis, endocarditis and toxic shock, and thus have a great impact on human health. The transformation of S. aureus from a colonization state to a pathogenic state during its life cycle is intimately associated with the initiation of bacterial aggregation and biofilm accumulation. SdrC, an S. aureus surface protein, can act as an adhesin to promote cell attachment and aggregation by an unknown mechanism. Her...
Source: Acta Crystallographica Section F - February 2, 2021 Category: Biochemistry Authors: Wang, J. Zhang, M. Wang, M. Zang, J. Zhang, X. Hang, T. Tags: Staphylococcus aureus adhesion SdrC dimer homophilic interaction research communications Source Type: research
Sleuthing biochemical evidence to elucidate unassigned electron density in a CBL – SLAP2 crystal complex
The Src-like adaptor proteins (SLAP/SLAP2) bind to CBL E3 ubiquitin ligase to downregulate antigen, cytokine and tyrosine kinase receptor signalling. In contrast to the phosphotyrosine-dependent binding of CBL substrates through its tyrosine kinase-binding domain (TKBD), CBL TKBD associates with the C-terminal tail of SLAP2 in a phospho-independent manner. To understand the distinct nature of this interaction, a purification protocol for SLAP2 in complex with CBL TKBD was established and the complex was crystallized. However, determination of the complex crystal structure was hindered by the apparent degradation of SLAP2 d...
Source: Acta Crystallographica Section F - February 1, 2021 Category: Biochemistry Authors: Wybenga-Groot, L.E. McGlade, C.J. Tags: unknown unassigned electron density protein – protein interaction feature-enhanced map E3 ubiquitin ligase adaptor proteins mass spectrometry research communications Source Type: research
Crystal structure of human V-1 in the apo form
V-1, also known as myotrophin, is a 13 kDa ankyrin-repeat protein that binds and inhibits the heterodimeric actin capping protein (CP), which is a key regulator of cytoskeletal actin dynamics. The crystal structure of V-1 in complex with CP revealed that V-1 recognizes CP via residues spanning several ankyrin repeats. Here, the crystal structure of human V-1 is reported in the absence of the specific ligand at 2.3 Å resolution. In the asymmetric unit, the crystal contains two V-1 monomers that exhibit nearly identical structures (C α r.m.s.d. of 0.47 Å ). The overall structures of the two apo ...
Source: Acta Crystallographica Section F - January 1, 2021 Category: Biochemistry Authors: Takeda, S. Koike, R. Nagae, T. Fujiwara, I. Narita, A. Ma é da, Y. Ota, M. Tags: V-1 myotrophin actin capping protein crystal structure All Atom Motion Tree ankyrin-repeat proteins research communications Source Type: research
Expression, purification and crystallization of the N-terminal Solanaceae domain of the Sw-5b NLR immune receptor
Plant nucleotide-binding domain and leucine-rich repeat receptors (NLRs) play crucial roles in recognizing pathogen effectors and activating plant immunity. The tomato NLR Sw-5b is a coiled-coil NLR (CC-NLR) immune receptor that confers resistance against tospoviruses, which cause serious economic losses in agronomic crops worldwide. Compared with other CC-NLRs, Sw-5b possesses an extended N-terminal Solanaceae domain (SD). The SD of Sw-5b is critical for recognition of the tospovirus viral movement protein NSm. An SD is also frequently detected in many NLRs from Solanaceae plants. However, no sequences homologous to the S...
Source: Acta Crystallographica Section F - December 23, 2020 Category: Biochemistry Authors: Li, J. Xin, J. Zhao, X. Zhao, Y. Wang, T. Xing, W. Tao, X. Tags: Sw-5b Solanaceae domain plant immune receptor Tomato spotted wilt orthotospovirus research communications Source Type: research
Using yeast surface display to engineer a soluble and crystallizable construct of hematopoietic progenitor kinase 1 (HPK1)
In this study, yeast surface display was applied to a library of HPK1 kinase-domain variants in order to select variants with an improved expression level and solubility. The HPK1 variant with the most improved properties contained two mutations, crystallized readily in complex with several small-molecule inhibitors and provided valuable insight to guide structure-based drug design. This work exemplifies the benefit of yeast surface display towards engineering crystallizable proteins and thus enabling structure-based drug discovery. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - December 22, 2020 Category: Biochemistry Authors: Lau, W.L. Pearce, B. Malakian, H. Rodrigo, I. Xie, D. Gao, M. Marsilio, F. Chang, C. Ruzanov, M. Muckelbauer, J.K. Newitt, J.A. Lipov š ek, D. Sheriff, S. Tags: hematopoietic progenitor kinase 1 HPK1 homology modeling yeast surface display crystallizability methods communications Source Type: research
A fully automated crystallization apparatus for small protein quantities
In 2003, a fully automated protein crystallization and monitoring system (PXS) was developed to support the structural genomics projects that were initiated in the early 2000s. In PXS, crystallization plates were automatically set up using the vapor-diffusion method, transferred to incubators and automatically observed according to a pre-set schedule. The captured images of each crystallization drop could be monitored through the internet using a web browser. While the screening throughput of PXS was very high, the demands of users have gradually changed over the ensuing years. To study difficult proteins, it has become im...
Source: Acta Crystallographica Section F - December 18, 2020 Category: Biochemistry Authors: Kato, R. Hiraki, M. Yamada, Y. Tanabe, M. Senda, T. Tags: crystallization automation high-throughput membrane proteins methods communications Source Type: research
Structural analysis of the chicken FANCM – MHF complex and its stability
FANCM is involved in eukaryotic DNA-damage recognition and activates the Fanconi anemia (FA) pathway through complex formation. MHF is one of the FANCM-associating components and contains a histone-fold DNA-binding domain. Loss of the FANCM – MHF interaction compromises the activation of the FA pathway, resulting in chromosomal instability. Thus, formation of the FANCM – MHF complex is important for function, but its nature largely remains elusive. Here, the aim was to reveal the molecular and structural basis for the stability of the FANCM – MHF complex. A recombinant tripartite complex containing chicke...
Source: Acta Crystallographica Section F - December 18, 2020 Category: Biochemistry Authors: Ito, S. Nishino, T. Tags: histone fold DNA binding DNA repair protein complex X-ray crystallography research communications Source Type: research
The hypothetical periplasmic protein PA1624 from Pseudomonas aeruginosa folds into a unique two-domain structure
The crystal structure of the 268-residue periplasmic protein PA1624 from the opportunistic pathogen Pseudomonas aeruginosa PAO1 was determined to high resolution using the Se-SAD method for initial phasing. The protein was found to be monomeric and the structure consists of two domains, domains 1 and 2, comprising residues 24 – 184 and 185 – 268, respectively. The fold of these domains could not be predicted even using state-of-the-art prediction methods, and similarity searches revealed only a very distant homology to known structures, namely to Mog1p/PsbP-like and OmpA-like proteins for the N- and C-terminal ...
Source: Acta Crystallographica Section F - November 30, 2020 Category: Biochemistry Authors: Feiler, C.G. Weiss, M.S. Blankenfeldt, W. Tags: periplasmic proteins unique folds unknown function human pathogenic bacteria potential drug targets Pseudomonas aeruginosa research communications Source Type: research
Crystallization of a nonclassical Kazal-type Carcinoscorpius rotundicauda serine protease inhibitor, CrSPI-1, complexed with subtilisin. Corrigendum
The name of the first author in the article by Tulisas et al. [(2009), Acta Cryst. F65, 533 – 535] is corrected. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - November 27, 2020 Category: Biochemistry Authors: Shenoy, R.T. Thangamani, S. Ho, B. Sivaraman, J. Ding, J.L. Tags: serine proteases Kazal-type serine protease inhibitors CrSPI corrigendum addenda and errata Source Type: research
Computer-controlled liquid-nitrogen drizzling device for removing frost from cryopreserved crystals
Cryocrystallography is a technique that is used more often than room-temperature data collection in macromolecular crystallography. One of its advantages is the significant reduction in radiation damage, which is especially useful in synchrotron experiments. Another advantage is that cryopreservation provides simple storage of crystals and easy transportation to a synchrotron. However, this technique sometimes results in the undesirable adhesion of frost to mounted crystals. The frost produces noisy diffraction images and reduces the optical visibility of crystals, which is crucial for aligning the crystal position with th...
Source: Acta Crystallographica Section F - November 25, 2020 Category: Biochemistry Authors: Nakamura, Y. Baba, S. Mizuno, N. Irie, T. Ueno, G. Hirata, K. Ito, S. Hasegawa, K. Yamamoto, M. Kumasaka, T. Tags: protein crystallography cryocrystallography removal of frost liquid-nitrogen drizzling device automated data collection methods communications Source Type: research
ATP-dependent RNA helicase domain of the ZC3H41 protein from Trypanosoma brucei: expression, purification and crystallization
A fragment of the Trypanosoma brucei ZC3H41 protein encompassing the ATP-dependent RNA helicase domain was successfully subcloned for expression in a bacterial system (Escherichia coli). Following expression, the protein was purified and crystallized using the vapor-diffusion method. The protein crystals were optimized at a 1:1 protein:reservoir solution ratio using PPGBA 2000. The optimized crystals diffracted to a dmin of 3.15 Å . The collected data revealed preliminary structural information regarding this newly discovered protein. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - November 25, 2020 Category: Biochemistry Authors: Izhaki-Tavor, L.S. Dessau, M. Tags: Trypanosoma brucei ATP-dependent RNA helicases ZC3H41 helicase C domain protozoan proteins DEAD-box proteins research communications Source Type: research
The crystal structure of benzophenone synthase from Garcinia mangostana L. pericarps reveals the basis for substrate specificity and catalysis
Benzophenone synthase (BPS) catalyzes the production of 2,4,6-trihydroxybenzophenone via the condensation of benzoyl-CoA and three units of malonyl-CoA. The biosynthetic pathway proceeds with the formation of the prenylated xanthone α -mangostin from 2,4,6-trihydroxybenzophenone. Structural elucidation was performed to gain a better understanding of the structural basis of the function of Garcinia mangostana L. (mangosteen) BPS (GmBPS). The structure reveals the common core consisting of a five-layer α β α β α fold as found in other type III polyketide synthase enzymes. The three residues ...
Source: Acta Crystallographica Section F - November 25, 2020 Category: Biochemistry Authors: Songsiriritthigul, C. Nualkaew, N. Ketudat-Cairns, J. Chen, C.-J. Tags: benzophenone synthase Garcinia mangostana L. 2,4,6-trihydroxybenzophenone polyketide synthases cyclization reaction research communications Source Type: research
Crystal structure of barley agmatine coumaroyltransferase, an N-acyltransferase from the BAHD superfamily
The enzymes of the BAHD superfamily, a large group of acyl-CoA-dependent acyltransferases in plants, are involved in the biosynthesis of diverse secondary metabolites. While the structures of several O-acyltransferases from the BAHD superfamily, such as hydroxycinnamoyl-CoA shikimate hydroxycinnamoyl transferase, have been elucidated, no structural information on N-acyltransferases is available. Hordeum vulgare agmatine coumaroyltransferase (HvACT) is an N-acyltransferase from the BAHD superfamily and is one of the most important enzymes in the secondary metabolism of barley. Here, an apo-form structure of HvACT is reporte...
Source: Acta Crystallographica Section F - November 25, 2020 Category: Biochemistry Authors: Yamane, M. Takenoya, M. Yajima, S. Sue, M. Tags: agmatine coumaroyltransferase BAHD superfamily Hordeum vulgare N-acyltransferases research communications Source Type: research
The X-ray crystal structure of the N-terminal domain of Ssr4, a Schizosaccharomyces pombe chromatin-remodelling protein
Ssr4 is a yeast protein from Schizosaccharomyces pombe and is an essential part of the chromatin-remodelling [SWI/SNF and RSC (remodelling the structure of chromatin)] complexes found in S. pombe. These complexes (or their homologues) regulate gene expression in eukaryotic organisms, affecting a large number of genes both positively and negatively. The downstream effects are seen in development, and in humans have implications for disease such as cancer. The chromatin structure is altered by modifying the DNA – histone contacts, thus opening up or closing down sections of DNA to specific transcription factors that re...
Source: Acta Crystallographica Section F - November 25, 2020 Category: Biochemistry Authors: Newman, J. Nebl, T. Van, H. Peat, T.S. Tags: chromatin remodelling SAD phasing novel structure Schizosaccharomyces pombe research communications Source Type: research
The A component (SmhA) of a tripartite pore-forming toxin from Serratia marcescens: expression, purification and crystallographic analysis
Tripartite α -pore-forming toxins are constructed of three proteins (A, B and C) and are found in many bacterial pathogens. While structures of the B and C components from Gram-negative bacteria have been described, the structure of the A component of a Gram-negative α -pore-forming toxin has so far proved elusive. SmhA, the A component from the opportunistic human pathogen Serratia marcescens, has been cloned, overexpressed and purified. Crystals were grown of selenomethionine-derivatized protein and anomalous data were collected. Phases were calculated and an initial electron-density map was produced. (Source...
Source: Acta Crystallographica Section F - November 25, 2020 Category: Biochemistry Authors: Churchill-Angus, A.M. Sedelnikova, S.E. Schofield, T.H.B. Baker, P.J. Tags: pore-forming toxin crystallization ClyA family Serratia research communications Source Type: research
Structural characterization of a nonhydrolyzing UDP-GlcNAc 2-epimerase from Neisseria meningitidis serogroup A
Bacterial nonhydrolyzing UDP-N-acetylglucosamine 2-epimerases catalyze the reversible interconversion of UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-N-acetylmannosamine (UDP-ManNAc). UDP-ManNAc is an important intermediate in the biosynthesis of certain cell-surface polysaccharides, including those in some pathogenic bacteria, such as Neisseria meningitidis and Streptococcus pneumoniae. Many of these epimerases are allosterically regulated by UDP-GlcNAc, which binds adjacent to the active site and is required to initiate UDP-ManNAc epimerization. Here, two crystal structures of UDP-N-acetylglucosamine 2-epimerase from Nei...
Source: Acta Crystallographica Section F - October 29, 2020 Category: Biochemistry Authors: Hurlburt, N.K. Guan, J. Ong, H. Yu, H. Chen, X. Fisher, A.J. Tags: UDP-GlcNAc UDP-ManNAc epimerases epimerization Rossmann fold X-ray crystallography Neisseria meningitidis research communications Source Type: research
Crystal structure of the GDP-bound GTPase domain of Rab5a from Leishmania donovani
Eukaryotic Rab5s are highly conserved small GTPase-family proteins that are involved in the regulation of early endocytosis. Leishmania donovani Rab5a regulates the sorting of early endosomes that are involved in the uptake of essential nutrients through fluid-phase endocytosis. Here, the 1.80 Å resolution crystal structure of the N-terminal GTPase domain of L. donovani Rab5a in complex with GDP is presented. The crystal structure determination was enabled by the design of specific single-site mutations and two deletions that were made to stabilize the protein for previous NMR studies. The structure of LdRab5a sh...
Source: Acta Crystallographica Section F - October 29, 2020 Category: Biochemistry Authors: Zohib, M. Maheshwari, D. Pal, R.K. Freitag-Pohl, S. Biswal, B.K. Pohl, E. Arora, A. Tags: Leishmania donovani fluid-phase endocytosis early endosomes Rab5a crystal structure research communications Source Type: research
Chitoporin from Serratia marcescens: recombinant expression, purification and crystallization
This study reports the identification of a chitoporin (ChiP), termed SmChiP, from the outer membrane of S. marcescens. Sequence alignment with genetically characterized ChiPs suggests that SmChiP is more closely related to the monomeric EcChiP from Escherichia coli than to the trimeric VhChiP from Vibrio campbellii. A single crystal of SmChiP grown under the condition 22%(w/v) PEG 8000, 0.1 M calcium acetate, 0.1 M MES pH 6.0 diffracted X-ray synchrotron radiation to 1.85 Å resolution. SmChiP co-crystallized with chitohexaose under the condition 19%(w/v) PEG 1500, 2 M ammonium phosphate monobasic, 0.1...
Source: Acta Crystallographica Section F - October 29, 2020 Category: Biochemistry Authors: Amornloetwattana, R. Robinson, R.C. Soysa, H.S.M. van den Berg, B. Suginta, W. Tags: chitin chitoporin outer membrane proteins Serratia marcescens sugar transport chitoligosaccharides sugar-specific porins research communications Source Type: research
Structural and biochemical characterization of the class II fructose-1,6-bisphosphatase from Francisella tularensis
The crystal structure of the class II fructose-1,6-bisphosphatase (FBPaseII) from the important pathogen Francisella tularensis is presented at 2.4 Å resolution. Its structural and functional relationships to the closely related phosphatases from Mycobacterium tuberculosis (MtFBPaseII) and Escherichia coli (EcFBPaseII) and to the dual phosphatase from Synechocystis strain 6803 are discussed. FBPaseII from F. tularensis (FtFBPaseII) was crystallized in a monoclinic crystal form (space group P21, unit-cell parameters a = 76.30, b = 100.17, c = 92.02 Å , β = 90.003 ° ) ...
Source: Acta Crystallographica Section F - October 23, 2020 Category: Biochemistry Authors: Selezneva, A.I. Gutka, H.J. Wolf, N.M. Qurratulain, F. Movahedzadeh, F. Abad-Zapatero, C. Tags: class II FBPases fructose-1,6-bisphophatase Mycobacterium tuberculosis Francisella tularensis antibiotic targets research communications Source Type: research
X-ray structure analysis of a unique d-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA
In this study, ReDAAO was crystallized by the hanging-drop vapor-diffusion method and its crystal structure was determined at a resolution of 2.00 Å . The crystal structure of the enzyme revealed that unlike other DAAOs, ReDAAO forms a homotetramer and contains an intramolecular disulfide bond (Cys230 – Cys285), suggesting that this disulfide bond is involved in the higher thermal stability of ReDAAO. Moreover, the structure of the active site and its vicinity in ReDAAO indicates that Arg97, Lys99, Lys114 and Ser231 are candidates for recognizing the side chain of d-Glu. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - October 23, 2020 Category: Biochemistry Authors: Shimekake, Y. Hirato, Y. Funabashi, R. Okazaki, S. Goto, M. Furuichi, T. Suzuki, H. Kera, Y. Takahashi, S. Tags: d-amino-acid oxidases flavoenzymes d-amino acids substrate specificity thermal stability thermophilic fungi Rasamsonia emersonii research communications Source Type: research
Alternative conformation of the C-domain of the P140 protein from Mycoplasma genitalium
The human pathogen Mycoplasma genitalium is responsible for urethritis in men, and for cervicitis and pelvic inflammatory disease in women. The adherence of M. genitalium to host target epithelial cells is mediated through an adhesion complex called Nap, which is essential for infectivity. Nap is a transmembrane dimer of heterodimers of the immunodominant proteins P110 and P140. The M. genitalium genome contains multiple copies of portions that share homology with the extracellular regions of P140 and P110 encoded by the genes mg191 and mg192, respectively. Homologous recombination between the genes and the c...
Source: Acta Crystallographica Section F - October 9, 2020 Category: Biochemistry Authors: Vizarraga, D. P é rez-Luque, R. Mart í n, J. Fita, I. Aparicio, D. Tags: Mycoplasma genitalium adhesins Nap gliding motility infection research communications Source Type: research
Multi-crystal data collection using synchrotron radiation as exemplified with low-symmetry crystals of Dps
Multi-crystal data collection using synchrotron radiation was successfully applied to determine the three-dimensional structure of a triclinic crystal form of Dps from Escherichia coli at 2.0 Å resolution. The final data set was obtained by combining 261 partial diffraction data sets measured from crystals with an average size of approximately 5 µ m. The most important features of diffraction data measurement and processing for low-symmetry crystals are discussed. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - October 8, 2020 Category: Biochemistry Authors: Kovalenko, V. Popov, A. Santoni, G. Loiko, N. Tereshkina, K. Tereshkin, E. Krupyanskii, Y. Tags: protein crystallography muti-crystal data collection clustering analysis methods communications Source Type: research
Structure of the substrate-binding domain of Plasmodium falciparum heat-shock protein 70-x
The malaria parasite Plasmodium falciparum extensively modifies erythrocytes that it invades by exporting a large complement of proteins to the host cell. Among these exported components is a single heat-shock 70 kDa class protein, PfHsp70-x, that supports the virulence and growth rate of the parasite during febrile episodes. The ATP-binding domain of PfHsp70-x has previously been resolved and showed the presence of potentially druggable epitopes that differ from those on human Hsp70 chaperones. Here, the crystallographic structure of the substrate-binding domain (SBD) of PfHsp70-x is presented in complex with a hydrop...
Source: Acta Crystallographica Section F - September 27, 2020 Category: Biochemistry Authors: Schmidt, J. Vakonakis, I. Tags: malaria chaperones Plasmodium falciparum erythrocyte remodelling PfHsp70-x PfEMP-1 crystallography complexes research communications Source Type: research
Crystal structure of XCC3289 from Xanthomonas campestris: homology with the N-terminal substrate-binding domain of Lon peptidase
LonA peptidase is a major component of the protein quality-control mechanism in both prokaryotes and the organelles of eukaryotes. Proteins homologous to the N-terminal domain of LonA peptidase, but lacking its other domains, are conserved in several phyla of prokaryotes, including the Xanthomonadales order. However, the function of these homologous proteins (LonNTD-like proteins) is not known. Here, the crystal structure of the LonNTD-like protein from Xanthomonas campestris (XCC3289; UniProt Q8P5P7) is reported at 2.8 Å resolution. The structure was solved by molecular replacement and contains one polypeptide i...
Source: Acta Crystallographica Section F - September 15, 2020 Category: Biochemistry Authors: Singh, R. Deshmukh, S. Kumar, A. Goyal, V.D. Makde, R.D. Tags: LonA cereblon protein binding XCC3289 Xanthomonas campestris research communications Source Type: research
Room-temperature neutron and X-ray data collection of 3CL Mpro from SARS-CoV-2
The replication of SARS-CoV-2 produces two large polyproteins, pp1a and pp1ab, that are inactive until cleavage by the viral chymotrypsin-like cysteine protease enzyme (3CL Mpro) into a series of smaller functional proteins. At the heart of 3CL Mpro is an unusual catalytic dyad formed by the side chains of His41 and Cys145 and a coordinated water molecule. The catalytic mechanism by which the enzyme operates is still unknown, as crucial information on the protonation states within the active site is unclear. To experimentally determine the protonation states of the catalytic site and of the other residues in the substrate-...
Source: Acta Crystallographica Section F - September 14, 2020 Category: Biochemistry Authors: Kneller, D.W. Phillips, G. Kovalevsky, A. Coates, L. Tags: neutron diffraction X-ray diffraction SARS-CoV-2 3CL Mpro research communications Source Type: research
A new soaking procedure for X-ray crystallographic structural determination of protein – peptide complexes
Interactions between a protein and a peptide motif of its protein partner are prevalent in nature. Often, a protein also has multiple interaction partners. X-ray protein crystallography is commonly used to examine these interactions in terms of bond distances and angles as well as to describe hotspots within protein complexes. However, the crystallization process presents a significant bottleneck in structure determination since it often requires notably time-consuming screening procedures, which involve testing a broad range of crystallization conditions via a trial-and-error approach. This difficulty is also increased as...
Source: Acta Crystallographica Section F - September 14, 2020 Category: Biochemistry Authors: Ballone, A. Lau, R.A. Zweipfenning, F.P.A. Ottmann, C. Tags: co-crystallization crystal soaking protein – peptide complexes research communications Source Type: research
Multiple crystal forms of human MacroD2
In this study, new crystallization conditions for MacroD2 were found and three crystal structures of human MacroD2 in the apo state were solved in space groups P41212, P43212 and P43, and refined at 1.75, 1.90 and 1.70 Å resolution, respectively. Structural comparison of the apo crystal structures with the previously reported crystal structure of MacroD2 in complex with ADP-ribose revealed conformational changes in the side chains of Val101, Ile189 and Phe224 induced by the binding of ADP-ribose in the active site. These conformational variations may potentially facilitate design efforts of a MacroD2 inhibitor. (...
Source: Acta Crystallographica Section F - September 14, 2020 Category: Biochemistry Authors: Wazir, S. Maksimainen, M.M. Lehti ö , L. Tags: macrodomain ADP-ribosylation ADP-ribosyl-hydrolase crystal forms apo structure research communications Source Type: research
Crystallization and structure of ebselen bound to Cys141 of human inositol monophosphatase
Inositol monophosphatase (IMPase) is inhibited by lithium, which is the most efficacious treatment for bipolar disorder. Several therapies have been approved, or are going through clinical trials, aimed at the replacement of lithium in the treatment of bipolar disorder. One candidate small molecule is ebselen, a selenium-containing antioxidant, which has been demonstrated to produce lithium-like effects both in a murine model and in clinical trials. Here, the crystallization and the first structure of human IMPase covalently complexed with ebselen, a 1.47 Å resolution crystal structure (PDB entry 6zk0), are prese...
Source: Acta Crystallographica Section F - September 14, 2020 Category: Biochemistry Authors: Fenn, G.D. Waller-Evans, H. Atack, J.R. Bax, B.D. Tags: inositol monophosphatase IMPase ebselen bipolar disorder tetramer research communications Source Type: research
The coiled-coil domain of glycosomal membrane-associated Leishmania donovani PEX14: cloning, overexpression, purification and preliminary crystallographic analysis
The glycosomal membrane-associated Leishmania donovani protein PEX14, which plays a crucial role in protein import from the cytosol to the glycosomal matrix, consists of three domains: an N-terminal domain where the signalling molecule binds, a transmembrane domain and an 84-residue coiled-coil domain (CC) that is responsible for oligomerization. CCs are versatile domains that participate in a variety of functions including supramolecular assembly, cellular signalling and transport. Recombinant PEX14 CC was cloned, overexpressed, affinity-purified with in-column thrombin cleavage and further purified by size-exclusion chro...
Source: Acta Crystallographica Section F - September 14, 2020 Category: Biochemistry Authors: Shakya, A.K. Pratap, J.V. Tags: Leishmania donovani coiled-coil domain PEX14 peroxisomes glycosomes research communications Source Type: research
Contamination or serendipity – doing the wrong thing by chance
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 31, 2020 Category: Biochemistry Authors: Newman, J. van Raaij, M.J. Tags: contaminants editorial Source Type: research
Detecting the nature and solving the crystal structure of a contaminant protein from an opportunistic pathogen
The unintentional crystallization of contaminant proteins in the place of target recombinant proteins is sporadically reported, despite the availability of stringent expression/purification protocols and of software for the detection of contaminants. Typically, the contaminant protein originates from the expression organism (for example Escherichia coli), but in rare circumstances contaminants from different sources have been reported. Here, a case of contamination from a Serratia bacterial strain that occurred while attempting to crystallize an unrelated protein from Burkholderia pseudomallei (overexpressed in E. coli) is...
Source: Acta Crystallographica Section F - August 27, 2020 Category: Biochemistry Authors: Pederzoli, R. Tarantino, D. Gourlay, L.J. Chaves-Sanjuan, A. Bolognesi, M. Tags: contaminant proteins cyanase hydratase Serratia research communications Source Type: research
The structure of the Moco carrier protein from Rippkaea orientalis
The molybdenum cofactor (Moco) is the prosthetic group of all molybdenum-dependent enzymes except for nitrogenase. The multistep biosynthesis pathway of Moco and its function in molybdenum-dependent enzymes are already well understood. The mechanisms of Moco transfer, storage and insertion, on the other hand, are not. In the cell, Moco is usually not found in its free form and remains bound to proteins because of its sensitivity to oxidation. The green alga Chlamydomonas reinhardtii harbors a Moco carrier protein (MCP) that binds and protects Moco but is devoid of enzymatic function. It has been speculated that this MCP ac...
Source: Acta Crystallographica Section F - August 27, 2020 Category: Biochemistry Authors: Krausze, J. Hercher, T.W. Archna, A. Kruse, T. Tags: molybdenum cofactor Moco carrier protein Rossmann fold molecular docking research communications Source Type: research