The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions

被引：33

作者：

Barth, S ^{[1
]}

Fischer, M ^{[1
]}

Schmid, RD ^{[1
]}

Pleiss, J ^{[1
]}

机构：

[1] Univ Stuttgart, Inst Tech Biochem, D-70569 Stuttgart, Germany

来源：

BIOINFORMATICS | 2004年 / 20卷 / 16期

关键词：

D O I：

10.1093/bioinformatics/bth284

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The epoxide hydrolases and haloalkane dehalogenases database (EH/HD) integrates sequence and structure of a highly diverse protein family, including mainly the Asp-hydrolases of EHs and HDs but also proteins, such as Ser-hydrolases non-heme peroxidases, prolyl iminopetidases and 2-hydroxymuconic semialdehyde hydrolases. These proteins have a highly conserved structure, but display a remarkable diversity in sequence and function. A total of 305 protein entries were assigned to 14 homologous families, forming two superfamilies. Annotated multisequence alignments and phylogenetic trees are provided for each homologous family and superfamily. Experimentally derived structures of 19 proteins are superposed and consistently annotated. Sequence and structure of all 305 proteins were systematically analysed. Thus, deeper insight is gained into the role of a highly conserved sequence motifs and structural elements.

引用

页码：2845 / 2847

页数：3

共 17 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] Sequence and structure of epoxide hydrolases: A systematic analysis [J].

Barth, S ;

Fischer, M ;

Schmid, RD ;

Pleiss, J .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2004, 55 (04) :846-855

[3] GenBank [J].

Benson, DA ;

Karsch-Mizrachi, I ;

Lipman, DJ ;

Ostell, J ;

Rapp, BA ;

Wheeler, DL .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :17-20

[4] The Protein Data Bank [J].

Berman, HM ;

Battistuz, T ;

Bhat, TN ;

Bluhm, WF ;

Bourne, PE ;

Burkhardt, K ;

Iype, L ;

Jain, S ;

Fagan, P ;

Marvin, J ;

Padilla, D ;

Ravichandran, V ;

Schneider, B ;

Thanki, N ;

Weissig, H ;

Westbrook, JD ;

Zardecki, C .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2002, 58 :899-907

[5] Purification and characterization of a prolyl aminopeptidase from Debaryomyces hansenii [J].

Bolumar, T ;

Sanz, Y ;

Aristoy, MC ;

Toldrá, F .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2003, 69 (01) :227-232

[6] Steady-state and pre-steady-state kinetic analysis of halopropane conversion by a Rhodococcus haloalkane dehalogenase [J].

Bosma, T ;

Pikkemaat, MG ;

Kingma, J ;

Dijk, J ;

Janssen, DB .

BIOCHEMISTRY, 2003, 42 (26) :8047-8053

[7] The Lipase Engineering Database: a navigation and analysis tool for protein families [J].

Fischer, M ;

Pleiss, J .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :319-321

[8] Alpha/Beta-Hydrolase Fold Enzymes: Structures, Functions and Mechanisms [J].

Holmquist, Mats .

CURRENT PROTEIN & PEPTIDE SCIENCE, 2000, 1 (02) :209-235

[9] DICTIONARY OF PROTEIN SECONDARY STRUCTURE - PATTERN-RECOGNITION OF HYDROGEN-BONDED AND GEOMETRICAL FEATURES [J].

KABSCH, W ;

SANDER, C .

BIOPOLYMERS, 1983, 22 (12) :2577-2637

[10] Metal-free bacterial haloperoxidases as unusual hydrolases: Activation of H2O2 by the formation of peracetic acid [J].

Picard, M ;

Gross, J ;

Lubbert, E ;

Tolzer, S ;

Krauss, S ;

vanPee, KH ;

Berkessel, A .

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION IN ENGLISH, 1997, 36 (11) :1196-1199

← 1 2 →