Site 2 of the Yersinia pestis substrate-binding protein YfeA is a dynamic surface metal-binding site
The substrate-binding protein YfeA (also known as YPO2439 or y1897) is a polyspecific metal-binding protein that is crucial for nutrient acquisition and virulence in Yersinia pestis, the causative microbe of plague. YfeA folds into a monomeric c-clamp like other substrate-binding proteins and has two metal-binding sites (sites 1 and 2). Site 2 is a bidentate surface site capable of binding Zn and Mn atoms and is a unique feature of YfeA. Occasionally, the site 2 residues of two YfeA molecules will cooperate with the histidine tag of a third YfeA molecule in coordinating the same metal and lead to metal-dependent crystallog...
Source: Acta Crystallographica Section F - August 24, 2021 Category: Biochemistry Authors: Radka, C.D. Aller, S.G. Tags: Yersinia pestis YfeA site 2 substrate-binding proteins inter-protein metal coordination crystallography zinc manganese transition-metal homeostasis plague research communications Source Type: research
Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments
Bacterial microcompartments are large supramolecular structures comprising an outer proteinaceous shell that encapsulates various enzymes in order to optimize metabolic processes. The outer shells of bacterial microcompartments are made of several thousand protein subunits, generally forming hexameric building blocks based on the canonical bacterial microcompartment (BMC) domain. Among the diverse metabolic types of bacterial microcompartments, the structures of those that use glycyl radical enzymes to metabolize choline have not been adequately characterized. Here, six structures of hexameric shell proteins from type I an...
Source: Acta Crystallographica Section F - August 24, 2021 Category: Biochemistry Authors: Ochoa, J.M. Mijares, O. Acosta, A.A. Escoto, X. Leon-Rivera, N. Marshall, J.D. Sawaya, M.R. Yeates, T.O. Tags: bacterial microcompartments bacterial organelles BMC shell proteins choline glycyl radicals research communications Source Type: research
The X-ray structure of l-threonine dehydrogenase from the common hospital pathogen Clostridium difficile
In many prokaryotes, the first step of threonine metabolism is catalysed by the enzyme threonine dehydrogenase (TDH), which uses NAD+ to oxidize its substrate to 2-amino-3-ketobutyrate. The absence of a functional TDH gene in humans suggests that inhibitors of this enzyme may have therapeutic potential against pathogens which are reliant on this enzyme. Here, TDH from Clostridium difficile has been cloned and overexpressed, and the X-ray structure of the apoenzyme form has been determined at 2.6 Å resolution. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 28, 2021 Category: Biochemistry Authors: Adjogatse, E. Bennett, J. Guo, J. Erskine, P.T. Wood, S.P. Wren, B.W. Cooper, J.B. Tags: threonine dehydrogenase Clostridium difficile protein crystallography molecular replacement refinement research communications Source Type: research
Structures of the Plasmodium falciparum heat-shock protein 70-x ATPase domain in complex with chemical fragments identify conserved and unique binding sites
Plasmodium falciparum invades erythrocytes and extensively modifies them in a manner that increases the virulence of this malaria parasite. A single heat-shock 70 kDa-type chaperone, PfHsp70-x, is among the parasite proteins exported to the host cell. PfHsp70-x assists in the formation of a key protein complex that underpins parasite virulence and supports parasite growth during febrile episodes. Previous work resolved the crystallographic structures of the PfHsp70-x ATPase and substrate-binding domains, and showed them to be highly similar to those of their human counterparts. Here, 233 chemical fragments were screene...
Source: Acta Crystallographica Section F - July 28, 2021 Category: Biochemistry Authors: Mohamad, N. O'Donoghue, A. Kantsadi, A.L. Vakonakis, I. Tags: Plasmodium falciparum PfHsp70-x heat-shock proteins malaria chaperones erythrocyte remodelling crystallography complexes fragment screening research communications Source Type: research
The identification and structural analysis of potential 14-3-3 interaction sites on the bone regulator protein Schnurri-3
14-3-3 proteins regulate many intracellular processes and their ability to bind in subtly different fashions to their numerous partner proteins provides attractive drug-targeting points for a range of diseases. Schnurri-3 is a suppressor of mouse bone formation and a candidate target for novel osteoporosis therapeutics, and thus it is of interest to determine whether it interacts with 14-3-3. In this work, potential 14-3-3 interaction sites on mammalian Schnurri-3 were identified by an in silico analysis of its protein sequence. Using fluorescence polarization, isothermal titration calorimetry and X-ray crystallography,...
Source: Acta Crystallographica Section F - July 28, 2021 Category: Biochemistry Authors: Soini, L. Leysen, S. Crabbe, T. Davis, J. Ottmann, C. Tags: bone regulator protein Schnurri-3 X-ray protein crystallography phosphorylation fluorescence polarization disulfide bonds 14-3-3 modes research communications Source Type: research
Conformational changes of loops highlight a potential binding site in Rhodococcus equi VapB
Virulence-associated proteins (Vaps) contribute to the virulence of the pathogen Rhodococcus equi, but their mode of action has remained elusive. All Vaps share a conserved core of about 105 amino acids that folds into a compact eight-stranded antiparallel β -barrel with a unique topology. At the top of the barrel, four loops connect the eight β -strands. Previous Vap structures did not show concave surfaces that might serve as a ligand-binding site. Here, the structure of VapB in a new crystal form was determined at 1.71 Å resolution. The asymmetric unit contains two molecules. In one of them, the loop regions at t...
Source: Acta Crystallographica Section F - July 28, 2021 Category: Biochemistry Authors: Geerds, C. Haas, A. Niemann, H.H. Tags: β -barrels ligand-binding sites conformational change virulence factors virulence-associated proteins Rhodococcus equi research communications Source Type: research
LrpCBA pilus proteins of gut-dwelling Ligilactobacillus ruminis: crystallization and X-ray diffraction analysis
Adhesion to host surfaces for bacterial survival and colonization involves a variety of molecular mechanisms. Ligilactobacillus ruminis, a strict anaerobe and gut autochthonous (indigenous) commensal, relies on sortase-dependent pili (LrpCBA) for adherence to the intestinal inner walls, thereby withstanding luminal content flow. Here, the LrpCBA pilus is a promiscuous binder to gut collagen, fibronectin and epithelial cells. Structurally, the LrpCBA pilus displays a representative hetero-oligomeric arrangement and consists of three types of pilin subunit, each with its own location and function, i.e. tip LrpC for adhesion,...
Source: Acta Crystallographica Section F - July 28, 2021 Category: Biochemistry Authors: Prajapati, A. Palva, A. von Ossowski, I. Krishnan, V. Tags: Ligilactobacillus ruminis autochthonous commensals intestine gut bacteria LrpCBA pilus pilins tip LrpC basal LrpB backbone LrpA research communications Source Type: research
Crystal structure of the TLDc domain of human NCOA7-AS
The TLDc [Tre2/Bub2/Cdc16 (TBC), lysin motif (LysM), domain catalytic] domain is associated with oxidation-resistance related functions and is well conserved among eukaryotes. Seven proteins possess a TLDc domain in humans, notably proteins belonging to the oxidation resistance protein (OXR), nuclear receptor coactivator 7 (NCOA7) and TBC1 domain family member 24 (TBC1D24) families. Although the mechanism is unknown, a protective role of TLDc proteins against oxidative stress, notably in the brain, has been demonstrated. Neurobiological disorders caused by mutations in the TLDc domain have also been reported. The human NCO...
Source: Acta Crystallographica Section F - July 28, 2021 Category: Biochemistry Authors: Arnaud-Arnould, M. Tauziet, M. Moncorg é , O. Goujon, C. Blaise, M. Tags: viral restriction factors oxidation resistance TLDc human NCOA7-AS research communications Source Type: research
Crystal structures of Val58Ile tryptophan repressor in a domain-swapped array in the presence and absence of l-tryptophan
The crystal structures of domain-swapped tryptophan repressor (TrpR) variant Val58Ile before and after soaking with the physiological ligand l-tryptophan (l-Trp) indicate that l-Trp occupies the same location in the domain-swapped form as in native dimeric TrpR and makes equivalent residue contacts. This result is unexpected because the ligand binding-site residues arise from three separate polypeptide chains in the domain-swapped form. This work represents the first published structure of a domain-swapped form of TrpR with l-Trp bound. The presented structures also show that the protein amino-terminus, whether or not it b...
Source: Acta Crystallographica Section F - June 30, 2021 Category: Biochemistry Authors: Sprenger, J. Lawson, C.L. von Wachenfeldt, C. Lo Leggio, L. Carey, J. Tags: crystalline protein gel hostal system fragment-based screening ligand binding molecular baits domain swapping Val58Ile tryptophan repressor research communications Source Type: research
PAIREF: paired refinement also for Phenix users
In macromolecular crystallography, paired refinement is generally accepted to be the optimal approach for the determination of the high-resolution cutoff. The software tool PAIREF provides automation of the protocol and associated analysis. Support for phenix.refine as a refinement engine has recently been implemented in the program. This feature is presented here using previously published data for thermolysin. The results demonstrate the importance of the complete cross-validation procedure to obtain a thorough and unbiased insight into the quality of high-resolution data. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 29, 2021 Category: Biochemistry Authors: Mal ý , M. Diederichs, K. Dohn á lek, J. Kolenko, P. Tags: macromolecular crystallography PAIREF Phenix X-ray diffraction paired refinement high-resolution limit methods communications Source Type: research
Structure of an H3N2 influenza virus nucleoprotein
Influenza A viruses of the H1N1 and H3N2 subtypes are responsible for seasonal epidemic events. The influenza nucleoprotein (NP) binds to the viral genomic RNA and is essential for its replication. Efforts are under way to produce therapeutics and vaccines targeting the NP. Despite this, no structure of an NP from an H3N2 virus has previously been determined. Here, the structure of the A/Northern Territory/60/1968 (H3N2) influenza virus NP is presented at 2.2 Å resolution. The structure is highly similar to those of the A/WSN/1933 (H1N1) and A/Hong Kong/483/97 (H5N1) NPs. Nonconserved amino acids are widely dispersed ...
Source: Acta Crystallographica Section F - June 29, 2021 Category: Biochemistry Authors: Knight, M.L. Fan, H. Bauer, D.L.V. Grimes, J.M. Fodor, E. Keown, J.R. Tags: influenza H3N2 influenza virus nucleoprotein X-ray crystallography RNA-binding protein research communications Source Type: research
Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4
This article reports the use of native intrinsic phosphorus and sulfur single-wavelength anomalous dispersion methods to solve the complex of the DNA-binding domain (DBD) of interferon regulatory factor 4 (IRF4) bound to its interferon-stimulated response element (ISRE). The structure unexpectedly shows three molecules of the IRF4 DBD bound to one ISRE. The sole reliance on native intrinsic anomalous scattering elements that belong to DNA – protein complexes renders the method of general applicability to a large number of such protein complexes that cannot be solved by molecular replacement or by other phasing methods. (...
Source: Acta Crystallographica Section F - June 29, 2021 Category: Biochemistry Authors: Agnarelli, A. El Omari, K. Duman, R. Wagner, A. Mancini, E.J. Tags: experimental phasing native SAD phosphorus DNA DNA-binding proteins IRF4 interferon regulatory factor 4 research communications Source Type: research
Crystal structures of HER3 extracellular domain 4 in complex with the designed ankyrin-repeat protein D5
The members of the human epidermal growth factor receptor (HER) family are among the most intensely studied oncological targets. HER3 (ErbB3), which had long been neglected, has emerged as a key oncogene, regulating the activity of other receptors and being involved in progression and tumor escape in multiple types of cancer. Designed ankyrin-repeat proteins (DARPins) serve as antibody mimetics that have proven to be useful in the clinic, in diagnostics and in research. DARPins have previously been selected against EGFR (HER1), HER2 and HER4. In particular, their combination into bivalent binders that separate or lock rece...
Source: Acta Crystallographica Section F - June 29, 2021 Category: Biochemistry Authors: Radom, F. Vonrhein, C. Mittl, P.R.E. Pl ü ckthun, A. Tags: protein engineering DARPins HER3 EGFR family tumor targeting research communications Source Type: research
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 sizes of the tw...
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
