The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases

被引：110

作者：

Knoll, Michael ^{[1
]}

Hamm, Thomas M. ^{[1
]}

Wagner, Florian ^{[1
]}

Martinez, Virginia ^{[2
]}

Pleiss, Juergen ^{[1
]}

机构：

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

[2] Ctr Invest Biol Ramiro de Maeztu, Dept Mol Microbiol, Madrid 28040, Spain

来源：

BMC BIOINFORMATICS | 2009年 / 10卷

关键词：

EXTRACELLULAR POLY(3-HYDROXYBUTYRATE) DEPOLYMERASE; MOLECULAR CHARACTERIZATION; POLYHYDROXYBUTYRATE DEPOLYMERASE; PSEUDOMONAS-LEMOIGNEI; GENE; PROTEIN; CLONING; DEGRADATION; SEQUENCE; IDENTIFICATION;

D O I：

10.1186/1471-2105-10-89

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: Polyhydroxyalkanoates (PHAs) can be degraded by many microorganisms using intra- or extracellular PHA depolymerases. PHA depolymerases are very diverse in sequence and substrate specificity, but share a common alpha/beta-hydrolase fold and a catalytic triad, which is also found in other alpha/beta-hydrolases. Results: The PHA Depolymerase Engineering Database (DED, http://www.ded.uni-stuttgart.de) has been established as a tool for systematic analysis of this enzyme family. The DED contains sequence entries of 587 PHA depolymerases, which were assigned to 8 superfamilies and 38 homologous families based on their sequence similarity. For each family, multiple sequence alignments and profile hidden Markov models are provided, and functionally relevant residues are annotated. Conclusion: The DED is a valuable tool which can be applied to identify new PHA depolymerase sequences from complete genomes in silico, to classify PHA depolymerases, to predict their biochemical properties, and to design enzyme variants with improved properties.

引用

页数：8

共 47 条

[1] Properties of a novel intracellular poly(3-hydroxybutyrate) depolymerase with high specific activity (PhaZd) in Wautersia eutropha H16 [J].

Abe, T ;

Kobayashi, T ;

Saito, T .

JOURNAL OF BACTERIOLOGY, 2005, 187 (20) :6982-6990

[2] 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

[3] OCCURRENCE, METABOLISM, METABOLIC ROLE, AND INDUSTRIAL USES OF BACTERIAL POLYHYDROXYALKANOATES [J].

ANDERSON, AJ ;

DAWES, EA .

MICROBIOLOGICAL REVIEWS, 1990, 54 (04) :450-472

[4]

Bateman A, 2002, NUCLEIC ACIDS RES, V30, P276, DOI [10.1093/nar/gkh121, 10.1093/nar/gkr1065, 10.1093/nar/gkp985]

[5] Poly(3-hydroxybutyrate) depolymerases bind to their substrate by a C-terminal located substrate binding site [J].

Behrends, A ;

Klingbeil, B ;

Jendrossek, D .

FEMS MICROBIOLOGY LETTERS, 1996, 143 (2-3) :191-194

[6]

Benson DA, 2017, NUCLEIC ACIDS RES, V45, pD37, DOI [10.1093/nar/gkp1024, 10.1093/nar/gkw1070, 10.1093/nar/gkq1079, 10.1093/nar/gkl986, 10.1093/nar/gkr1202, 10.1093/nar/gkx1094, 10.1093/nar/gks1195, 10.1093/nar/gkn723, 10.1093/nar/gkg057]

[7] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[8]

Briese Bernd Holger, 1994, Journal of Environmental Polymer Degradation, V2, P75, DOI 10.1007/BF02074776

[9] EXTRACELLULAR POLY(3-HYDROXYBUTYRATE) DEPOLYMERASE FROM PENICILLIUM-FUNICULOSUM - GENERAL-CHARACTERISTICS AND ACTIVE-SITE STUDIES [J].

BRUCATO, CL ;

WONG, SS .

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 1991, 290 (02) :497-502

[10] Biochemical evidence that phaZ gene encodes a specific intracellular medium chain length polyhydroxyalkanoate depolymerase in Pseudomonas putida KT2442 -: Characterization of a paradigmatic enzyme [J].

de Eugenio, Laura I. ;

Garcia, Pedro ;

Luengo, Jose M. ;

Sanz, Jesus M. ;

San Roman, Julio ;

Garcia, Jose Luis ;

Prieto, Maria A. .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2007, 282 (07) :4951-4962

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