Crystal structure of chorismate mutase from Burkholderia phymatum

Asojo, Oluwatoyin A.; Subramanian, Sandhya; Abendroth, Jan; Exley, Ilyssa; Lorimer, Donald D.; Edwards, Thomas E.; Myler, Peter J.

doi:10.1107/S2053230X18002868

Title: Crystal structure of chorismate mutase from Burkholderia phymatum

Journal Article · Thu Mar 22 00:00:00 EDT 2018 · Acta Crystallographica. Section F, Structural Biology Communications

DOI:https://doi.org/10.1107/S2053230X18002868· OSTI ID:1498432

; Subramanian, Sandhya; Abendroth, Jan; Exley, Ilyssa; Lorimer, Donald D.; Edwards, Thomas E.;

The bacterium Burkholderia phymatum is a promiscuous symbiotic nitrogen-fixating bacterium that belongs to one of the largest groups of Betaproteobacteria. Other Burkholderia species are known to cause disease in plants and animals, and some are potential agents for biological warfare. Structural genomics efforts include characterizing the structures of enzymes from pathways that can be targeted for drug development. As part of these efforts, chorismate mutase from B. phymatum was produced and crystallized, and a 1.95 Å resolution structure is reported. This enzyme shares less than 33% sequence identity with other homologs of known structure. There are two classes of chorismate mutase: AroQ and AroH. The bacterial subclass AroQγ has reported roles in virulence. Chorismate mutase from B. phymatum has the prototypical AroQγ topology and retains the characteristic chorismate mutase active site. This suggests that substrate-based chorismate mutase inhibitors will not be specific and are likely to affect beneficial bacteria such as B. phymatum.

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Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: NIAIDNIH

OSTI ID:: 1498432

Journal Information:: Acta Crystallographica. Section F, Structural Biology Communications, Vol. 74, Issue 4; ISSN 2053-230X

Publisher:: International Union of Crystallography

Country of Publication:: United States

Language:: ENGLISH

References (31)

PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Ligation-independent cloning of PCR products (LIC-PCR) Aslanidis, Charalampos; de Jong, Pieter J. Nucleic Acids Research, Vol. 18, Issue 20 https://doi.org/10.1093/nar/18.20.6069	journal	January 1990
Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome Baugh, Loren; Gallagher, Larry A.; Patrapuvich, Rapatbhorn PLoS ONE, Vol. 8, Issue 1 https://doi.org/10.1371/journal.pone.0053851	journal	January 2013
High-throughput protein production and purification at the Seattle Structural Genomics Center for Infectious Disease Bryan, Cassie M.; Bhandari, Janhavi; Napuli, Alberto J. Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 67, Issue 9 https://doi.org/10.1107/S1744309111018367	journal	August 2011
Immobilized metal-affinity chromatography protein-recovery screening is predictive of crystallographic structure success Choi, Ryan; Kelley, Angela; Leibly, David Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 67, Issue 9 https://doi.org/10.1107/S1744309111017374	journal	August 2011
Experiences with the shikimate-pathway enzymes as targets for rational drug design Coggins, J. R.; Abell, C.; Evans, L. B. Biochemical Society Transactions, Vol. 31, Issue 3 https://doi.org/10.1042/bst0310548	journal	June 2003
Research Status and Prospect of Burkholderia glumae, the Pathogen Causing Bacterial Panicle Blight Zhou-qi, Cui; Bo, Zhu; Guan-lin, Xie Rice Science, Vol. 23, Issue 3 https://doi.org/10.1016/j.rsci.2016.01.007	journal	May 2016
ESPript: analysis of multiple sequence alignments in PostScript Gouet, P.; Courcelle, E.; Stuart, D. Bioinformatics, Vol. 15, Issue 4 https://doi.org/10.1093/bioinformatics/15.4.305	journal	April 1999
ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins Gouet, P. Nucleic Acids Research, Vol. 31, Issue 13 https://doi.org/10.1093/nar/gkg556	journal	July 2003
Understanding the Role of Active-Site Residues in Chorismate Mutase Catalysis from Molecular-Dynamics Simulations Guo, Hong; Cui, Qiang; Lipscomb, William N. Angewandte Chemie International Edition, Vol. 42, Issue 13 https://doi.org/10.1002/anie.200219878	journal	April 2003
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Mycobacterium tuberculosis chorismate mutase: A potential target for TB Khanapur, Manjulatha; Alvala, Mallika; Prabhakar, Maddela Bioorganic & Medicinal Chemistry, Vol. 25, Issue 6 https://doi.org/10.1016/j.bmc.2017.02.001	journal	March 2017
A comparative biochemical and structural analysis of the intracellular chorismate mutase (Rv0948c) from Mycobacterium tuberculosis H37Rv and the secreted chorismate mutase (y2828) from Yersinia pestis: AroQ chorismate mutases Kim, Sook-Kyung; Reddy, Sathyavelu K.; Nelson, Bryant C. FEBS Journal, Vol. 275, Issue 19 https://doi.org/10.1111/j.1742-4658.2008.06621.x	journal	August 2008
Biochemical and Structural Characterization of the Secreted Chorismate Mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv: an *AroQ Enzyme Not Regulated by the Aromatic Amino Acids Kim, S. -K.; Reddy, S. K.; Nelson, B. C. Journal of Bacteriology, Vol. 188, Issue 24 https://doi.org/10.1128/JB.00441-06	journal	December 2006
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Krissinel, E.; Henrick, K. Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12 https://doi.org/10.1107/S0907444904026460	journal	November 2004
Model preparation in MOLREP and examples of model improvement using X-ray data Lebedev, Andrey A.; Vagin, Alexei A.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S0907444907049839	journal	December 2007
Atomic structure of the buried catalytic pocket of Escherichia coli chorismate mutase Lee, Angela Y.; Karplus, P. Angrew; Ganem, Bruce Journal of the American Chemical Society, Vol. 117, Issue 12 https://doi.org/10.1021/ja00117a038	journal	March 1995
Complete Genome sequence of Burkholderia phymatum STM815T, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species Moulin, Lionel; Klonowska, Agnieszka; Caroline, Bournaud Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.4861021	journal	March 2014
The Seattle Structural Genomics Center for Infectious Disease (SSGCID) Myler, P.; Stacy, R.; Stewart, L. Infectious Disorders - Drug Targets, Vol. 9, Issue 5 https://doi.org/10.2174/187152609789105687	journal	October 2009
1.6Å Crystal Structure of the Secreted Chorismate Mutase from Mycobacterium tuberculosis: Novel Fold Topology Revealed Ökvist, Mats; Dey, Raja; Sasso, Severin Journal of Molecular Biology, Vol. 357, Issue 5 https://doi.org/10.1016/j.jmb.2006.01.069	journal	April 2006
The 2.15 Å Crystal Structure of Mycobacterium tuberculosis Chorismate Mutase Reveals an Unexpected Gene Duplication and Suggests a Role in Host−Pathogen Interactions ^† Qamra, Rohini; Prakash, Prachee; Aruna, Bandi Biochemistry, Vol. 45, Issue 23 https://doi.org/10.1021/bi0606445	journal	June 2006
Gene design, cloning and protein-expression methods for high-value targets at the Seattle Structural Genomics Center for Infectious Disease Raymond, Amy; Haffner, Taryn; Ng, Nathan Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 67, Issue 9 https://doi.org/10.1107/S1744309111026698	journal	August 2011
Evidence for the shikimate pathway in apicomplexan parasites Roberts, Fiona; Roberts, Craig W.; Johnson, Jennifer J. Nature, Vol. 393, Issue 6687 https://doi.org/10.1038/31723	journal	June 1998
Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species Sawana, Amandeep; Adeolu, Mobolaji; Gupta, Radhey S. Frontiers in Genetics, Vol. 5 https://doi.org/10.3389/fgene.2014.00429	journal	December 2014
Structure of an ADP-ribosylation factor, ARF1, from Entamoeba histolytica bound to Mg ²⁺ –GDP Serbzhinskiy, Dmitry A.; Clifton, Matthew C.; Sankaran, Banumathi Acta Crystallographica Section F Structural Biology Communications, Vol. 71, Issue 5 https://doi.org/10.1107/S2053230X15004677	journal	April 2015
Structural genomics of infectious disease drug targets: the SSGCID Stacy, Robin; Begley, Darren W.; Phan, Isabelle Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 67, Issue 9 https://doi.org/10.1107/S1744309111029204	journal	August 2011
Protein production by auto-induction in high-density shaking cultures Studier, F. William Protein Expression and Purification, Vol. 41, Issue 1, p. 207-234 https://doi.org/10.1016/j.pep.2005.01.016	journal	May 2005
Investigation of Potential Inhibitors of Chorismate-Utilizing Enzymes Svarcova, Marketa; Kratky, Martin; Vinsova, Jarmila Current Medicinal Chemistry, Vol. 22, Issue 11 https://doi.org/10.2174/0929867322666150209152446	journal	March 2015
Molecular replacement with MOLREP Vagin, Alexei; Teplyakov, Alexei Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042589	journal	December 2009
Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., Nodulate the Roots of Tropical Legumes Vandamme, Peter; Goris, Johan; Chen, Wen-Ming Systematic and Applied Microbiology, Vol. 25, Issue 4 https://doi.org/10.1078/07232020260517634	journal	January 2002
Proposal of Burkholderia gen. nov. and Transfer of Seven Species of the Genus Pseudomonas Homology Group II to the New Genus, with the Type Species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Yabuuchi, Eiko; Kosako, Yoshimasa; Oyaizu, Hiroshi Microbiology and Immunology, Vol. 36, Issue 12 https://doi.org/10.1111/j.1348-0421.1992.tb02129.x	journal	December 1992

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