Joanna Hale

Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.

BtDyP from Bacteroides thetaiotaomicron (strain VPI‐5482) and TyrA from Shewanella oneidensis are dye‐decolorizing peroxidases (DyPs), members of a new family of heme‐dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 Å, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two‐domain, α+β ferredoxin‐like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme‐binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein). Proteins 2007.

Structural Basis of Murein Peptide Specificity of a γ-D-glutamyl-L-diamino Acid Endopeptidase

The crystal structures of two homologous endopeptidases from cyanobacteria Anabaena variabilis and Nostoc punctiforme were determined at 1.05 and 1.60 A resolution, respectively, and contain a bacterial SH3-like domain (SH3b) and a ubiquitous cell-wall-associated NlpC/P60 (or CHAP) cysteine peptidase domain. The NlpC/P60 domain is a primitive, papain-like peptidase in the CA clan of cysteine peptidases with a Cys126/His176/His188 catalytic triad and a conserved catalytic core. We deduced from structure and sequence analysis, and then experimentally, that these two proteins act as gamma-D-glutamyl-L-diamino acid endopeptidases (EC 3.4.22.-). The active site is located near the interface between the SH3b and NlpC/P60 domains, where the SH3b domain may help define substrate specificity, instead of functioning as a targeting domain, so that only muropeptides with an N-terminal L-alanine can bind to the active site.

Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 Å resolution reveals a new fold

Chris Rife, Robert Schwarzenbacher, Daniel McMullan, Polat Abdubek, Eileen Ambing, Herbert Axelrod, Tanya Biorac, Jaume M. Canaves, Hsiu-Ju Chiu, Ashley M. Deacon, Michael DiDonato, Marc-André Elsliger, Adam Godzik, Carina Grittini, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Gye Won Han, Justin Haugen, Michael Hornsby, Lukasz Jaroszewski, Heath E. Klock, Eric Koesema, Andreas Kreusch, Peter Kuhn, Scott A. Lesley, Mitchell D. Miller, Kin Moy, Edward Nigoghossian, Jessica Paulsen, Kevin Quijano, Ron Reyes, Eric Sims, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, Jeff Velasquez, Juli Vincent, Aprilfawn White, Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, and Ian A. Wilson* The Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California The University of California, San Diego, La Jolla, California The Genomics Institute of the Novartis Research Foundation, San Diego, California The Scripps Research Institute, La Jolla, California

Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 Å resolution

Qingping Xu, Robert Schwarzenbacher, S. Sri Krishna, Daniel McMullan, Sanjay Agarwalla, Kevin Quijano, Polat Abdubek, Eileen Ambing, Herbert Axelrod, Tanya Biorac, Jaume M. Canaves, Hsiu-Ju Chiu, Marc-André Elsliger, Carina Grittini, Slawomir K. Grzechnik, Michael DiDonato, Joanna Hale, Eric Hampton, Gye Won Han, Justin Haugen, MichaelHornsby, Lukasz Jaroszewski, Heath E. Klock, Mark W. Knuth, Eric Koesema, Andreas Kreusch, Peter Kuhn, Mitchell D. Miller, Kin Moy, Edward Nigoghossian, Jessica Paulsen, Ron Reyes, Chris Rife, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, Jeff Velasquez, Aprilfawn White, Guenter Wolf, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, and Ian A. Wilson* The Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California The University of California San Diego, La Jolla, California The Genomics Institute of the Novartis Research Foundation, San Diego, California The Scripps Research Institute, La Jolla, California

Crystal structure of an indigoidine synthase A (IndA)‐like protein (TM1464) from Thermotoga maritima at 1.90 Å resolution reveals a new fold

Inna Levin, Mitchell D. Miller, Robert Schwarzenbacher, Daniel McMullan, Polat Abdubek, Eileen Ambing, Tanya Biorac, Jamison Cambell, Jaume M. Canaves, Hsiu-Ju Chiu, Ashley M. Deacon, Michael DiDonato, Marc-André Elsliger, Adam Godzik, Carina Grittini, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Gye Won Han, Justin Haugen, Michael Hornsby, Lukasz Jaroszewski, Cathy Karlak, Heath E. Klock, Eric Koesema, Andreas Kreusch, Peter Kuhn, Scott A. Lesley, Andrew Morse, Kin Moy, Edward Nigoghossian, Jie Ouyang, Rebecca Page, Kevin Quijano, Ron Reyes, Alyssa Robb, Eric Sims, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, Jeff Velasquez, Juli Vincent, Xianhong Wang, Bill West, Guenter Wolf, Qingping Xu, Olga Zagnitko, Keith O. Hodgson, John Wooley, and Ian A. Wilson* Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California San Diego Supercomputer Center, La Jolla, California Genomics Institute of the Novartis Research Foundation, San Diego, California University of California, San Diego, La Jolla, California Scripps Research Institute, La Jolla, California

A structural basis for the regulatory inactivation of DnaA.

Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174 and 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation that promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type of mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel beta-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP-bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda.

Crystal structure of a single‐stranded DNA‐binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution

Michael DiDonato, S. Sri Krishna, Robert Schwarzenbacher, Daniel McMullan, Lukasz Jaroszewski, Mitchell D. Miller, Polat Abdubek, Sanjay Agarwalla, Eileen Ambing, Herbert Axelrod, Tanya Biorac, Hsiu-Ju Chiu, Ashley M. Deacon, Marc-André Elsliger, Julie Feuerhelm, Adam Godzik, Carina Grittini, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Justin Haugen, Michael Hornsby, Heath E. Klock, Mark W. Knuth, Eric Koesema, Andreas Kreusch, Peter Kuhn, Scott A. Lesley, Kin Moy, Edward Nigoghossian, Linda Okach, Jessica Paulsen, Kevin Quijano, Ron Reyes, Chris Rife, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, Jeff Velasquez, Aprilfawn White, Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, and Ian A. Wilson Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California San Diego Supercomputer Center, La Jolla, California Genomics Institute of the Novartis Research Foundation, San Diego, California University of California, San Diego, La Jolla, California The Scripps Research Institute, La Jolla, California

Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution

Lukasz Jaroszewski, Robert Schwarzenbacher, Daniel McMullan, Polat Abdubek, Sanjay Agarwalla, Eileen Ambing, Herbert Axelrod, Tanya Biorac, Jaume M. Canaves, Hsiu-Ju Chiu, Ashley M. Deacon, Michael DiDonato, Marc-André Elsliger, Adam Godzik, Carina Grittini, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Gye Won Han, Justin Haugen, Michael Hornsby, Heath E. Klock, Eric Koesema, Andreas Kreusch, Peter Kuhn, Scott A. Lesley, Mitchell D. Miller, Kin Moy, Edward Nigoghossian, Jessica Paulsen, Kevin Quijano, Ron Reyes, Chris Rife, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, Jeff Velasquez, Juli Vincent, Aprilfawn White, Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, and Ian A. Wilson* The Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California The University of California, San Diego, La Jolla, California The Genomics Institute of the Novartis Research Foundation, San Diego, California The Scripps Research Institute, La Jolla, California

Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution.

Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 Å resolution Chloe Zubieta, S. Sri Krishna, Daniel McMullan, Mitchell D. Miller, Polat Abdubek, Sanjay Agarwalla, Eileen Ambing, Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton, Hsiu-Ju Chiu, Thomas Clayton, Marc Deller, Michael DiDonato, Lian Duan, Marc-André Elsliger, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Gye Won Han, Justin Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Eric Koesema, Abhinav Kumar, David Marciano, Andrew T. Morse, Edward Nigoghossian, Silvya Oommachen, Ron Reyes, Christopher L. Rife, Henry van den Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, and Ian A. Wilson* 1 Joint Center for Structural Genomics (JCSG) 2 Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California 3 Burnham Institute for Medical Research, La Jolla, California 4 Center for Research in Biological Systems, University of California, San Diego, La Jolla, California 5 Genomics Institute of the Novartis Research Foundation, San Diego, California 6 The Scripps Research Institute, La Jolla, California

Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution

Gye Won Han, S. Sri Krishna, Robert Schwarzenbacher, Daniel McMullan, Krzysztof Ginalski, Marc-André Elsliger, Scott M. Brittain, Polat Abdubek, Sanjay Agarwalla, Eileen Ambing, Tamara Astakhova, Herbert Axelrod, Jaume M. Canaves, Hsiu-Ju Chiu, Michael DiDonato, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Justin Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Eric Koesema, Andreas Kreusch, Peter Kuhn, Mitchell D. Miller, Andrew T. Morse, Kin Moy, Edward Nigoghossian, Sylvia Oommachen, Jie Ouyang, Jessica Paulsen, Kevin Quijano, Ron Reyes, Chris Rife, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, Jeff Velasquez, Xianhong Wang, Bill West, Aprilfawn White, Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, and Ian A. Wilson* Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California University of California, San Diego, La Jolla, California Genomics Institute of the Novartis Research Foundation, San Diego, California The Scripps Research Institute, La Jolla, California Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warsaw, Poland