Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 Å resolution

Naqvi, Kubra F.; Staker, Bart L.; Dobson, Renwick C.  J.; Serbzhinskiy, Dmitry; Sankaran, Banumathi; Myler, Peter J.; Hudson, André O.

doi:10.1107/S2053230X15023213

Title: Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 Å resolution

Journal Article · Fri Jan 01 00:00:00 EST 2016 · Acta Crystallographica. Section F, Structural Biology Communications

DOI:https://doi.org/10.1107/S2053230X15023213· OSTI ID:1378764

Naqvi, Kubra F. ^[1]; Staker, Bart L. ^[2]; Dobson, Renwick C. J. ^[3]; Serbzhinskiy, Dmitry ^[2]; Sankaran, Banumathi ^[4]; Myler, Peter J. ^[5]; Hudson, André O. ^[1]

Rochester Inst. of Technology, Rochester, NY (United States). Thomas H. Gosnell School of Life Sciences
Seattle Structural Genomics Center for Infectious Disease (United States); Center for Infectious Disease Research, Seattle, WA (United States)
Univ. of Canterbury, Christchurch (New Zealand). Biomolecular Interaction Centre, School of Biological Sciences
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Berkeley Center for Structural Biology
Seattle Structural Genomics Center for Infectious Disease (United States); Center for Infectious Disease Research, Seattle, WA (United States); Univ. of Washington, Seattle, WA (United States). Dept. of Global Health; Univ. of Washington, Seattle, WA (United States). Dept. of Biomedical Informatics and Health Education

The enzyme dihydrodipicolinate synthase catalyzes the committed step in the synthesis of diaminopimelate and lysine to facilitate peptidoglycan and protein synthesis. Dihydrodipicolinate synthase catalyzes the condensation of L-aspartate 4-semialdehyde and pyruvate to synthesize L-2,3-dihydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the pathogenic bacteriumBartonella henselae, the causative bacterium of cat-scratch disease, are presented. Protein crystals were grown in conditions consisting of 20%(w/v) PEG 4000, 100 mMsodium citrate tribasic pH 5.5 and were shown to diffract to ~2.10 Å resolution. They belonged to space groupP2₁2₁2₁, with unit-cell parametersa= 79.96,b= 106.33,c= 136.25 Å. The finalRvalues wereR_r.i.m.= 0.098,R_work= 0.183,R_free= 0.233.

View Journal Article

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)

DOE Contract Number:: AC02-05CH11231; HHSN272200700057C; HHSN272201200025C

OSTI ID:: 1378764

Journal Information:: Acta Crystallographica. Section F, Structural Biology Communications, Vol. 72, Issue 1; ISSN 2053-230X

Publisher:: International Union of Crystallography

Country of Publication:: United States

Language:: English

References (38)

Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis Kefala, Georgia; Evans, Genevieve L.; Griffin, Michael D. W. Biochemical Journal, Vol. 411, Issue 2 https://doi.org/10.1042/BJ20071360	journal	March 2008
Antibacterial activity of synthetic analogues based on the disaccharide structure of moenomycin, an inhibitor of bacterial transglycosylase Baizman, Eugene R.; Branstrom, Arthur A.; Longley, Clifford B. Microbiology, Vol. 146, Issue 12 https://doi.org/10.1099/00221287-146-12-3129	journal	December 2000
Structure of dihydrodipicolinate synthase from the commensal bacterium Bacteroides thetaiotaomicron at 2.1 Å resolution Mank, Nicholas; Arnette, Amy; Klapper, Vince Acta Crystallographica Section F Structural Biology Communications, Vol. 71, Issue 4 https://doi.org/10.1107/S2053230X15004628	journal	March 2015
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
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 Å resolution Blagova, Elena; Levdikov, Vladimir; Milioti, Natalia Proteins: Structure, Function, and Bioinformatics, Vol. 62, Issue 1 https://doi.org/10.1002/prot.20684	journal	November 2005
Biochemical studies and crystal structure determination of dihydrodipicolinate synthase from Pseudomonas aeruginosa Kaur, Navpreet; Gautam, Ankur; Kumar, Sanjit International Journal of Biological Macromolecules, Vol. 48, Issue 5 https://doi.org/10.1016/j.ijbiomac.2011.03.002	journal	June 2011
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
L,L-diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine McCoy, A. J.; Adams, N. E.; Hudson, A. O. Proceedings of the National Academy of Sciences, Vol. 103, Issue 47 https://doi.org/10.1073/pnas.0608643103	journal	November 2006
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
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
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
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
Genomic and Biochemical Analysis of the Diaminopimelate and Lysine Biosynthesis Pathway in Verrucomicrobium spinosum: Identification and Partial Characterization of L,L-Diaminopimelate Aminotransferase and UDP-N-Acetylmuramoylalanyl-D-glutamyl-2,6-meso-Diaminopimelate Ligase Nachar, Victoria R.; Savka, Francisco C.; McGroty, Sean E. Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00183	journal	January 2012
Cat-scratch disease: a wide spectrum of clinical pictures Mazur-Melewska, Katarzyna; Mania, Anna; Kemnitz, Paweł Advances in Dermatology and Allergology, Vol. 3 https://doi.org/10.5114/pdia.2014.44014	journal	January 2015
Structure of dihydrodipicolinate synthase of Nicotiana sylvestris reveals novel quaternary structure Blickling, Stefan; Beisel, Hans-Georg; Bozic, Damir Journal of Molecular Biology, Vol. 274, Issue 4 https://doi.org/10.1006/jmbi.1997.1393	journal	December 1997
The DAP pathway to lysine as a target for antimicrobial agents Cox, Russell J. Natural Product Reports, Vol. 13, Issue 1 https://doi.org/10.1039/np9961300029	journal	January 1996
L,L-diaminopimelate aminotransferase (DapL): a putative target for the development of narrow-spectrum antibacterial compounds Triassi, Alexander J.; Wheatley, Matthew S.; Savka, Michael A. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00509	journal	September 2014
Crystal, Solution and In silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine Atkinson, Sarah C.; Dogovski, Con; Downton, Matthew T. PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0038318	journal	June 2012
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
The Crystal Structure of Dihydrodipicolinate Synthase fromEscherichia coliat 2.5 Å Resolution Mirwaldt, Christian; Korndorfer, Ingo; Huber, Robert Journal of Molecular Biology, Vol. 246, Issue 1 https://doi.org/10.1006/jmbi.1994.0078	journal	February 1995
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
Biochemical and Phylogenetic Characterization of a Novel Diaminopimelate Biosynthesis Pathway in Prokaryotes Identifies a Diverged Form of LL-Diaminopimelate Aminotransferase Hudson, A. O.; Gilvarg, C.; Leustek, T. Journal of Bacteriology, Vol. 190, Issue 9 https://doi.org/10.1128/JB.01381-07	journal	February 2008
Inhibition of lysine biosynthesis: an evolving antibiotic strategy Hutton, Craig A.; Perugini, Matthew A.; Gerrard, Juliet A. Molecular BioSystems, Vol. 3, Issue 7 https://doi.org/10.1039/b705624a	journal	January 2007
Structure and Evolution of a Novel Dimeric Enzyme from a Clinically Important Bacterial Pathogen Burgess, Benjamin R.; Dobson, Renwick C. J.; Bailey, Michael F. Journal of Biological Chemistry, Vol. 283, Issue 41 https://doi.org/10.1074/jbc.M804231200	journal	August 2008
Regulatory mechanisms after short- and long-term perturbed lysine biosynthesis in the aspartate pathway: the need for isogenes in Arabidopsis thaliana Van Bochaute, Pieter; Novoa, Alexandre; Ballet, Steven Physiologia Plantarum, Vol. 149, Issue 4 https://doi.org/10.1111/ppl.12053	journal	April 2013
Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis Devenish, Sean R. A.; Huisman, Frances H. A.; Parker, Emily J. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1794, Issue 8 https://doi.org/10.1016/j.bbapap.2009.02.003	journal	August 2009
Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase Girish, Tavarekere S.; Sharma, Eshita; Gopal, B. FEBS Letters, Vol. 582, Issue 19 https://doi.org/10.1016/j.febslet.2008.07.035	journal	July 2008
Bartonella Infection in Animals: Carriership, Reservoir Potential, Pathogenicity, and Zoonotic Potential for Human Infection Breitschwerdt, E. B.; Kordick, D. L. Clinical Microbiology Reviews, Vol. 13, Issue 3 https://doi.org/10.1128/CMR.13.3.428-438.2000	journal	July 2000
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
Dihydrodipicolinate synthase from Thermotoga maritima Pearce, F. Grant; Perugini, Matthew A.; Mckerchar, Hannah J. Biochemical Journal, Vol. 400, Issue 2 https://doi.org/10.1042/BJ20060771	journal	November 2006
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
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
Role of Arginine 138 in the Catalysis and Regulation of Escherichia coli Dihydrodipicolinate Synthase ^† Dobson, Renwick C. J.; Devenish, Sean R. A.; Turner, Leighton A. Biochemistry, Vol. 44, Issue 39 https://doi.org/10.1021/bi051281w	journal	October 2005
An ll-Diaminopimelate Aminotransferase Defines a Novel Variant of the Lysine Biosynthesis Pathway in Plants Hudson, André O.; Singh, Bijay K.; Leustek, Thomas Plant Physiology, Vol. 140, Issue 1 https://doi.org/10.1104/pp.105.072629	journal	December 2005
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
The Crystal Structure of Three Site-directed Mutants of Escherichia coli Dihydrodipicolinate Synthase: Further Evidence for a Catalytic Triad Dobson, Renwick C. J.; Valegård, Karin; Gerrard, Juliet A. Journal of Molecular Biology, Vol. 338, Issue 2 https://doi.org/10.1016/j.jmb.2004.02.060	journal	April 2004

Similar Records

The purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum

Journal Article · Sat Mar 01 00:00:00 EST 2008 · Acta Crystallographica. Section F · OSTI ID:1378764

Dobson, Renwick C. J.,; Atkinson, Sarah C.; Gorman, Michael A.; +3 more

Purification, crystallization and preliminary X-ray diffraction studies to near-atomic resolution of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus

Journal Article · Tue Jul 01 00:00:00 EDT 2008 · Acta Crystallographica. Section F · OSTI ID:1378764

Burgess, Benjamin R.; Dobson, Renwick C. J.,; Dogovski, Con; +2 more

Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate

Journal Article · Sat Aug 13 00:00:00 EDT 2011 · Acta Crystallographica. Section F · OSTI ID:1378764

Gardberg, Anna; Abendroth, Jan; Bhandari, Janhavi; +2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Bartonella henselae
dihydrodipicolinate synthase
diaminopimelate
lysine biosynthesis
cat-scratch disease

Title: Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 Å resolution

Citation Formats

References (38)

Similar Records

Related Subjects