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 phenylalanine r...
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) is repor...
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, Phe...
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 the cyto...
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 invest...
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-crystall...
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 AGAP1...
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 clariflavu...
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, cadherin-...
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 structural fold...
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
