Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118.

The structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC188 has been determined at 1.72 Å resolution. The structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. Despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β D-ribose 5-phosphate isomerase fold. Comparison to other related structures revealed high homology in the active site, allowing a model of the substrate-bound protein to be proposed. The determination of the structure was expedited by the use of in situ crystallization-plate screening on beamline I04-1 at Diamond Light Source to identify well diffracting protein crystals prior to routine cryocrystallography.

[1]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[2]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[3]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[4]  A G Leslie,et al.  Biological Crystallography Integration of Macromolecular Diffraction Data , 2022 .

[5]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[6]  A. Matte,et al.  Crystal structure of D‐ribose‐5‐phosphate isomerase (RpiA) from Escherichia coli , 2002, Proteins.

[7]  Kazuhiko Ishikawa,et al.  A hyperthermostable D-ribose-5-phosphate isomerase from Pyrococcus horikoshii characterization and three-dimensional structure. , 2002, Structure.

[8]  Y. Nodake,et al.  Oxyanion Hole-stabilized Stereospecific Isomerization in Ribose-5-phosphate Isomerase (Rpi)* , 2003, Journal of Biological Chemistry.

[9]  Cheryl H Arrowsmith,et al.  Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle. , 2003, Structure.

[10]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[11]  A. Edwards,et al.  The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction. , 2003, Journal of molecular biology.

[12]  Slawomir K. Grzechnik,et al.  Crystal structure of a ribose‐5‐phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 Å resolution , 2004, Proteins.

[13]  Nicholas K. Sauter,et al.  Robust indexing for automatic data collection , 2004, Journal of applied crystallography.

[14]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[15]  T. A. Jones,et al.  Mycobacterium tuberculosis ribose-5-phosphate isomerase has a known fold, but a novel active site. , 2004, Journal of molecular biology.

[16]  Philippe Carpentier,et al.  Automated analysis of vapor diffusion crystallization drops with an X-ray beam. , 2004, Structure.

[17]  Philippe Carpentier,et al.  CATS: a Cryogenic Automated Transfer System installed on the beamline FIP at ESRF , 2004 .

[18]  F. Studier,et al.  Protein production by auto-induction in high density shaking cultures. , 2005, Protein expression and purification.

[19]  Lester G. Carter,et al.  A procedure for setting up high‐throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization , 2005, Acta crystallographica. Section D, Biological crystallography.

[20]  J. Janin,et al.  Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archaeal and bacterial enzymes. , 2005, Biochimie.

[21]  S. Mowbray,et al.  Competitive Inhibitors of Mycobacterium tuberculosis Ribose-5-phosphate Isomerase B Reveal New Information about the Reaction Mechanism* , 2005, Journal of Biological Chemistry.

[22]  T. Earnest,et al.  Structure of ribose 5-phosphate isomerase from Plasmodium falciparum. , 2006, Acta crystallographica. Section F, Structural biology and crystallization communications.

[23]  P. Evans,et al.  Scaling and assessment of data quality. , 2006, Acta crystallographica. Section D, Biological crystallography.

[24]  Nicholas K. Sauter,et al.  Automated diffraction image analysis and spot searching for high-throughput crystal screening , 2006 .

[25]  Ronan M Keegan,et al.  Automated search-model discovery and preparation for structure solution by molecular replacement. , 2007, Acta crystallographica. Section D, Biological crystallography.

[26]  David Alderton,et al.  A versatile ligation-independent cloning method suitable for high-throughput expression screening applications , 2007, Nucleic acids research.

[27]  V. Lamzin,et al.  Assessment of automatic ligand building in ARP/wARP , 2006, Acta crystallographica. Section D, Biological crystallography.

[28]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[29]  C. Hill,et al.  Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118 , 2007, Proceedings of the National Academy of Sciences.

[30]  N. Grishin,et al.  PROMALS3D: a tool for multiple protein sequence and structure alignments , 2008, Nucleic acids research.

[31]  Norman Stein,et al.  CHAINSAW: a program for mutating pdb files used as templates in molecular replacement , 2008 .

[32]  L Jacquamet,et al.  Upgrade of the CATS sample changer on FIP-BM30A at the ESRF: towards a commercialized standard. , 2009, Journal of synchrotron radiation.

[33]  C. Ban,et al.  Crystal structures of substrate and inhibitor complexes of ribose 5-phosphate isomerase A from Vibrio vulnificus YJ016 , 2009, Molecules and cells.

[34]  Fabrice Gorrec,et al.  The MORPHEUS protein crystallization screen , 2009, Journal of applied crystallography.

[35]  Y. Bessho,et al.  The structure of an archaeal ribose-5-phosphate isomerase from Methanocaldococcus jannaschii (MJ1603). , 2009, Acta crystallographica. Section F, Structural biology and crystallization communications.

[36]  S. Sainsbury,et al.  The structure of NMB1585, a MarR-family regulator from Neisseria meningitidis , 2009, Acta crystallographica. Section F, Structural biology and crystallization communications.

[37]  P. O’Toole,et al.  Probiotic properties of Lactobacillus salivarius and closely related Lactobacillus species. , 2010, Future microbiology.

[38]  Alexei Vagin,et al.  Molecular replacement with MOLREP. , 2010, Acta crystallographica. Section D, Biological crystallography.

[39]  Graeme Winter,et al.  xia2: an expert system for macromolecular crystallography data reduction , 2010 .

[40]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[41]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[42]  S. Mowbray,et al.  Structures of type B ribose 5‐phosphate isomerase from Trypanosoma cruzi shed light on the determinants of sugar specificity in the structural family , 2011, The FEBS journal.

[43]  L. Bird High throughput construction and small scale expression screening of multi-tag vectors in Escherichia coli. , 2011, Methods.

[44]  T. Tomizaki,et al.  SLS Crystallization Platform at Beamline X06DA—A Fully Automated Pipeline Enabling in Situ X-ray Diffraction Screening , 2011 .

[45]  G. Labesse,et al.  In-plate protein crystallization, in situ ligand soaking and X-ray diffraction. , 2011, Acta crystallographica. Section D, Biological crystallography.

[46]  L. Kang,et al.  Crystal structure of Clostridium thermocellum ribose-5-phosphate isomerase B reveals properties critical for fast enzyme kinetics , 2011, Applied Microbiology and Biotechnology.

[47]  Gwyndaf Evans,et al.  In situ macromolecular crystallography using microbeams , 2012, Acta crystallographica. Section D, Biological crystallography.

[48]  Gwyndaf Evans,et al.  A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71 , 2012, Nature Structural &Molecular Biology.

[49]  A manual low-cost protein-crystallization plate jig for in situ diffraction in the home laboratory , 2011, Journal of applied crystallography.

[50]  P. O’Toole,et al.  Influence of Adhesion and Bacteriocin Production by Lactobacillus salivarius on the Intestinal Epithelial Cell Transcriptional Response , 2012, Applied and Environmental Microbiology.