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Axelrod HL, Kozbial P, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Carlton D, Caruthers J, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Feuerhelm J, Grzechnik SK, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Tien HJ, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Zubieta C, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1347-53. [PMID: 20944231 PMCID: PMC2954225 DOI: 10.1107/s1744309109021988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 06/09/2009] [Indexed: 12/02/2022]
Abstract
In the plant pathogen Xanthomonas campestris pv. campestris, the product of the tcmJ gene, XcTcmJ, encodes a protein belonging to the RmlC family of cupins. XcTcmJ was crystallized in a monoclinic space group (C2) in the presence of zinc acetate and the structure was determined to 1.6 Å resolution. Previously, the apo structure has been reported in the absence of any bound metal ion [Chin et al. (2006), Proteins, 65, 1046-1050]. The most significant difference between the apo structure and the structure of XcTcmJ described here is a reorganization of the binding site for zinc acetate, which was most likely acquired from the crystallization solution. This site is located in the conserved metal ion-binding domain at the putative active site of XcTcmJ. In addition, an acetate was also bound within coordination distance of the zinc. In order to accommodate this binding, rearrangement of a conserved histidine ligand is required as well as several nearby residues within and around the putative active site. These observations indicate that binding of zinc serves a functional role in this cupin protein.
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Affiliation(s)
- Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Mitchell D. Miller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Claire Acosta
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan Caruthers
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Ylva Elias
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Slawomir K. Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kevin K. Jin
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Abhinav Kumar
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kevin D. Murphy
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Silvya Oommachen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jessica Paulsen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christopher L. Rife
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry J. Tien
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christina V. Trout
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Henry van den Bedem
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
| | - Aprilfawn White
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Chloe Zubieta
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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