Literature DB >> 10557275

Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family.

S Sinha1, P Rappu, S C Lange, P Mäntsälä, H Zalkin, J L Smith.   

Abstract

The yabJ gene in Bacillus subtilis is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The molecular mechanism of YabJ is unknown. YabJ is a member of a large, widely distributed family of proteins of unknown biochemical function. The 1.7-A crystal structure of YabJ reveals a trimeric organization with extensive buried hydrophobic surface and an internal water-filled cavity. The most important finding in the structure is a deep, narrow cleft between subunits lined with nine side chains that are invariant among the 25 most similar homologs. This conserved site is proposed to be a binding or catalytic site for a ligand or substrate that is common to YabJ and other members of the YER057c/YjgF/UK114 family of proteins.

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Year:  1999        PMID: 10557275      PMCID: PMC23902          DOI: 10.1073/pnas.96.23.13074

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  27 in total

1.  A role for a highly conserved protein of unknown function in regulation of Bacillus subtilis purA by the purine repressor.

Authors:  P Rappu; B S Shin; H Zalkin; P Mäntsälä
Journal:  J Bacteriol       Date:  1999-06       Impact factor: 3.490

2.  Template convolution to enhance or detect structural features in macromolecular electron-density maps.

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Authors:  A Nicholls; K A Sharp; B Honig
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4.  Interaction of Bacillus subtilis purine repressor with DNA.

Authors:  B S Shin; A Stein; H Zalkin
Journal:  J Bacteriol       Date:  1997-12       Impact factor: 3.490

5.  TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.

Authors:  A C Wallace; N Borkakoti; J M Thornton
Journal:  Protein Sci       Date:  1997-11       Impact factor: 6.725

6.  ALSCRIPT: a tool to format multiple sequence alignments.

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7.  The monofunctional chorismate mutase from Bacillus subtilis. Structure determination of chorismate mutase and its complexes with a transition state analog and prephenate, and implications for the mechanism of the enzymatic reaction.

Authors:  Y M Chook; J V Gray; H Ke; W N Lipscomb
Journal:  J Mol Biol       Date:  1994-07-29       Impact factor: 5.469

8.  Crystallization and preliminary X-ray diffraction studies of perchloric acid soluble protein (PSP) from rat liver.

Authors:  K Djinović Carugo; M Saraste; T Oka
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-03

9.  Dual role of alpha-acetolactate decarboxylase in Lactococcus lactis subsp. lactis.

Authors:  N Goupil-Feuillerat; M Cocaign-Bousquet; J J Godon; S D Ehrlich; P Renault
Journal:  J Bacteriol       Date:  1997-10       Impact factor: 3.490

10.  Identification of the Bacillus subtilis pur operon repressor.

Authors:  M Weng; P L Nagy; H Zalkin
Journal:  Proc Natl Acad Sci U S A       Date:  1995-08-01       Impact factor: 11.205

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  32 in total

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Authors:  George Schmitz; Diana M Downs
Journal:  J Bacteriol       Date:  2004-02       Impact factor: 3.490

2.  Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.

Authors:  Alexander Stark; Robert B Russell
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

3.  In vivo effect of mutations at the PRPP binding site of the Bacillus subtilis purine repressor.

Authors:  Pekka Rappu; Terhi Pullinen; Pekka Mäntsälä
Journal:  J Bacteriol       Date:  2003-11       Impact factor: 3.490

4.  Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions.

Authors:  Jennifer A Lambrecht; Jeffrey M Flynn; Diana M Downs
Journal:  J Biol Chem       Date:  2011-11-17       Impact factor: 5.157

5.  Crystallization and preliminary X-ray analysis of the YjgF/YER057c/UK114-family protein ST0811 from Sulfolobus tokodaii strain 7.

Authors:  Takuya Miyakawa; Ken Ichi Hatano; Woo Cheol Lee; Yusuke Kato; Yoriko Sawano; Fumiaki Yumoto; Koji Nagata; Masaru Tanokura
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2005-08-31

6.  YjgF is required for isoleucine biosynthesis when Salmonella enterica is grown on pyruvate medium.

Authors:  Melissa R Christopherson; G E Schmitz; Diana M Downs
Journal:  J Bacteriol       Date:  2008-02-22       Impact factor: 3.490

7.  Acid stress response of a mycobacterial proteome: insight from a gene ontology analysis.

Authors:  Bryan Ap Roxas; Qingbo Li
Journal:  Int J Clin Exp Med       Date:  2009-11-10

8.  The σB-dependent yabJ-spoVG operon is involved in the regulation of extracellular nuclease, lipase, and protease expression in Staphylococcus aureus.

Authors:  Bettina Schulthess; Dominik A Bloes; Patrice François; Myriam Girard; Jacques Schrenzel; Markus Bischoff; Brigitte Berger-Bächi
Journal:  J Bacteriol       Date:  2011-07-01       Impact factor: 3.490

Review 9.  RidA Proteins Protect against Metabolic Damage by Reactive Intermediates.

Authors:  Jessica L Irons; Kelsey Hodge-Hanson; Diana M Downs
Journal:  Microbiol Mol Biol Rev       Date:  2020-07-15       Impact factor: 11.056

10.  DUK114, the Drosophila orthologue of bovine brain calpain activator protein, is a molecular chaperone.

Authors:  Attila Farkas; Gábor Nardai; Peter Csermely; Peter Tompa; Peter Friedrich
Journal:  Biochem J       Date:  2004-10-01       Impact factor: 3.857

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