Literature DB >> 22865330

Solution NMR and X-ray crystal structures of Pseudomonas syringae Pspto_3016 from protein domain family PF04237 (DUF419) adopt a "double wing" DNA binding motif.

Erik A Feldmann1, Jayaraman Seetharaman, Theresa A Ramelot, Scott Lew, Li Zhao, Keith Hamilton, Colleen Ciccosanti, Rong Xiao, Thomas B Acton, John K Everett, Liang Tong, Gaetano T Montelione, Michael A Kennedy.   

Abstract

The protein Pspto_3016 is a 117-residue member of the protein domain family PF04237 (DUF419), which is to date a functionally uncharacterized family of proteins. In this report, we describe the structure of Pspto_3016 from Pseudomonas syringae solved by both solution NMR and X-ray crystallography at 2.5 Å resolution. In both cases, the structure of Pspto_3016 adopts a "double wing" α/β sandwich fold similar to that of protein YjbR from Escherichia coli and to the C-terminal DNA binding domain of the MotA transcription factor (MotCF) from T4 bacteriophage, along with other uncharacterized proteins. Pspto_3016 was selected by the Protein Structure Initiative of the National Institutes of Health and the Northeast Structural Genomics Consortium (NESG ID PsR293).

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Year:  2012        PMID: 22865330      PMCID: PMC3697073          DOI: 10.1007/s10969-012-9140-8

Source DB:  PubMed          Journal:  J Struct Funct Genomics        ISSN: 1345-711X


  29 in total

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Authors:  M Kanehisa; S Goto
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  The MotA transcription factor from bacteriophage T4 contains a novel DNA-binding domain: the 'double wing' motif.

Authors:  Ning Li; E Allen Sickmier; Rongguang Zhang; Andrzej Joachimiak; Stephen W White
Journal:  Mol Microbiol       Date:  2002-03       Impact factor: 3.501

3.  Electrostatics of nanosystems: application to microtubules and the ribosome.

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Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-21       Impact factor: 11.205

4.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Mol Biol       Date:  2002-05-24       Impact factor: 5.469

5.  Automated NMR structure calculation with CYANA.

Authors:  Peter Güntert
Journal:  Methods Mol Biol       Date:  2004

6.  Novel leverage of structural genomics.

Authors:  Jinfeng Liu; Gaetano T Montelione; Burkhard Rost
Journal:  Nat Biotechnol       Date:  2007-08       Impact factor: 54.908

7.  The complete genome sequence of Escherichia coli K-12.

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Journal:  Science       Date:  1997-09-05       Impact factor: 47.728

8.  Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

Authors:  G Cornilescu; F Delaglio; A Bax
Journal:  J Biomol NMR       Date:  1999-03       Impact factor: 2.835

9.  Solution structure of the transcriptional activation domain of the bacteriophage T4 protein, MotA.

Authors:  N Li; W Zhang; S W White; R W Kriwacki
Journal:  Biochemistry       Date:  2001-04-10       Impact factor: 3.162

10.  The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.

Authors:  Margaret J Gabanyi; Paul D Adams; Konstantin Arnold; Lorenza Bordoli; Lester G Carter; Judith Flippen-Andersen; Lida Gifford; Juergen Haas; Andrei Kouranov; William A McLaughlin; David I Micallef; Wladek Minor; Raship Shah; Torsten Schwede; Yi-Ping Tao; John D Westbrook; Matthew Zimmerman; Helen M Berman
Journal:  J Struct Funct Genomics       Date:  2011-04-07
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  4 in total

1.  Visualizing the phage T4 activated transcription complex of DNA and E. coli RNA polymerase.

Authors:  Tamara D James; Timothy Cardozo; Lauren E Abell; Meng-Lun Hsieh; Lisa M Miller Jenkins; Saheli S Jha; Deborah M Hinton
Journal:  Nucleic Acids Res       Date:  2016-07-25       Impact factor: 16.971

2.  Principal components analysis of protein sequence clusters.

Authors:  Bo Wang; Michael A Kennedy
Journal:  J Struct Funct Genomics       Date:  2014-02-05

3.  The phage T4 MotA transcription factor contains a novel DNA binding motif that specifically recognizes modified DNA.

Authors:  Maxime G Cuypers; Rosanna M Robertson; Leslie Knipling; M Brett Waddell; Kyung Moon; Deborah M Hinton; Stephen W White
Journal:  Nucleic Acids Res       Date:  2018-06-01       Impact factor: 16.971

4.  Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes.

Authors:  Ryan T Bell; Yuri I Wolf; Eugene V Koonin
Journal:  BMC Biol       Date:  2020-11-04       Impact factor: 7.431

  4 in total

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