Literature DB >> 17588214

Functional insights from structural genomics.

Farhad Forouhar1, Alexandre Kuzin, Jayaraman Seetharaman, Insun Lee, Weihong Zhou, Mariam Abashidze, Yang Chen, Wei Yong, Haleema Janjua, Yingyi Fang, Dongyan Wang, Kellie Cunningham, Rong Xiao, Thomas B Acton, Eran Pichersky, Daniel F Klessig, Carl W Porter, Gaetano T Montelione, Liang Tong.   

Abstract

Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF_0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP_1951), and a 12-stranded beta-barrel with a novel fold (V. parahaemolyticus VPA1032).

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Year:  2007        PMID: 17588214     DOI: 10.1007/s10969-007-9018-3

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


  46 in total

1.  Functional assignment based on structural analysis: crystal structure of the yggJ protein (HI0303) of Haemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot.

Authors:  Farhad Forouhar; Jianwei Shen; Rong Xiao; Thomas B Acton; Gaetano T Montelione; Liang Tong
Journal:  Proteins       Date:  2003-11-01

2.  A novel Bacillus subtilis gene involved in negative control of sporulation and degradative-enzyme production.

Authors:  M Honjo; A Nakayama; K Fukazawa; K Kawamura; K Ando; M Hori; Y Furutani
Journal:  J Bacteriol       Date:  1990-04       Impact factor: 3.490

3.  Structural and functional evidence for Bacillus subtilis PaiA as a novel N1-spermidine/spermine acetyltransferase.

Authors:  Farhad Forouhar; In-Sun Lee; Jelena Vujcic; Slavoljub Vujcic; Jianwei Shen; Sergey M Vorobiev; Rong Xiao; Thomas B Acton; Gaetano T Montelione; Carl W Porter; Liang Tong
Journal:  J Biol Chem       Date:  2005-10-06       Impact factor: 5.157

4.  Crystal structures of the tryptophan repressor binding protein WrbA and complexes with flavin mononucleotide.

Authors:  Jason Gorman; Lawrence Shapiro
Journal:  Protein Sci       Date:  2005-12       Impact factor: 6.725

5.  Biochemical characterization of WrbA, founding member of a new family of multimeric flavodoxin-like proteins.

Authors:  R Grandori; P Khalifah; J A Boice; R Fairman; K Giovanielli; J Carey
Journal:  J Biol Chem       Date:  1998-08-14       Impact factor: 5.157

6.  Crystallization and preliminary X-ray analysis of the 9 kDa protein of the mouse signal recognition particle and the selenomethionyl-SRP9.

Authors:  S Doublié; U Kapp; A Aberg; K Brown; K Strub; S Cusack
Journal:  FEBS Lett       Date:  1996-04-22       Impact factor: 4.124

7.  Identification of a Soluble, High-Affinity Salicylic Acid-Binding Protein in Tobacco.

Authors:  H. Du; D. F. Klessig
Journal:  Plant Physiol       Date:  1997-04       Impact factor: 8.340

8.  Characterization and pathogenic significance of Vibrio vulnificus antigens preferentially expressed in septicemic patients.

Authors:  Young Ran Kim; Shee Eun Lee; Choon Mee Kim; Soo Young Kim; Eun Kyoung Shin; Dong Hyeon Shin; Sun Sik Chung; Hyon E Choy; Ann Progulske-Fox; Jeffrey D Hillman; Martin Handfield; Joon Haeng Rhee
Journal:  Infect Immun       Date:  2003-10       Impact factor: 3.441

9.  Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643.

Authors:  Zhiru Yang; Alexei Savchenko; Alexander Yakunin; Rongguang Zhang; Aled Edwards; Cheryl Arrowsmith; Liang Tong
Journal:  J Biol Chem       Date:  2002-12-21       Impact factor: 5.157

10.  A novel NAD-binding protein revealed by the crystal structure of 2,3-diketo-L-gulonate reductase (YiaK).

Authors:  Farhad Forouhar; Insun Lee; Jordi Benach; Kaushal Kulkarni; Rong Xiao; Thomas B Acton; Gaetano T Montelione; Liang Tong
Journal:  J Biol Chem       Date:  2004-01-12       Impact factor: 5.157

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  24 in total

1.  Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment.

Authors:  Martin Sagermann; Akashi Ohtaki; Kiel Nikolakakis
Journal:  Proc Natl Acad Sci U S A       Date:  2009-05-18       Impact factor: 11.205

2.  Exploiting genomic patterns to discover new supramolecular protein assemblies.

Authors:  Morgan Beeby; Thomas A Bobik; Todd O Yeates
Journal:  Protein Sci       Date:  2009-01       Impact factor: 6.725

3.  Two new high-resolution crystal structures of carboxysome pentamer proteins reveal high structural conservation of CcmL orthologs among distantly related cyanobacterial species.

Authors:  Markus Sutter; Steven C Wilson; Samuel Deutsch; Cheryl A Kerfeld
Journal:  Photosynth Res       Date:  2013-08-15       Impact factor: 3.573

4.  Genetic analysis of the protein shell of the microcompartments involved in coenzyme B12-dependent 1,2-propanediol degradation by Salmonella.

Authors:  Shouqiang Cheng; Sharmistha Sinha; Chenguang Fan; Yu Liu; Thomas A Bobik
Journal:  J Bacteriol       Date:  2011-01-14       Impact factor: 3.490

5.  The 1:2 complex between RavZ and LC3 reveals a mechanism for deconjugation of LC3 on the phagophore membrane.

Authors:  Do Hoon Kwon; Sulhee Kim; Yang Ouk Jung; Kyung-Hye Roh; Leehyeon Kim; Byeong-Won Kim; Seung Beom Hong; In Young Lee; Ju Han Song; Woo Cheol Lee; Eui-Ju Choi; Kwang Yeon Hwang; Hyun Kyu Song
Journal:  Autophagy       Date:  2016-10-28       Impact factor: 16.016

Review 6.  Diverse bacterial microcompartment organelles.

Authors:  Chiranjit Chowdhury; Sharmistha Sinha; Sunny Chun; Todd O Yeates; Thomas A Bobik
Journal:  Microbiol Mol Biol Rev       Date:  2014-09       Impact factor: 11.056

7.  Interactions and structural variability of β-carboxysomal shell protein CcmL.

Authors:  Thomas J Keeling; Bożena Samborska; Ryan W Demers; Matthew S Kimber
Journal:  Photosynth Res       Date:  2014-02-07       Impact factor: 3.573

8.  Role and Function of LitR, an Adenosyl B12-Bound Light-Sensitive Regulator of Bacillus megaterium QM B1551, in Regulation of Carotenoid Production.

Authors:  Hideaki Takano; Kou Mise; Kenta Hagiwara; Naoya Hirata; Shoko Watanabe; Minami Toriyabe; Hatsumi Shiratori-Takano; Kenji Ueda
Journal:  J Bacteriol       Date:  2015-04-27       Impact factor: 3.490

9.  PROFESS: a PROtein function, evolution, structure and sequence database.

Authors:  Thomas Triplet; Matthew D Shortridge; Mark A Griep; Jaime L Stark; Robert Powers; Peter Revesz
Journal:  Database (Oxford)       Date:  2010-07-06       Impact factor: 3.451

10.  Microcompartments for B12-dependent 1,2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate.

Authors:  Edith M Sampson; Thomas A Bobik
Journal:  J Bacteriol       Date:  2008-02-22       Impact factor: 3.490

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