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 its clo...
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 V-1 chains are ...
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 chicken FANCM (MHF...
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 domains,...
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 Met264, Tyr266 and Gly339 ar...
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 regula...
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
