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R ing‐ H ydroxylating O xygenase database: a database of bacterial aromatic ring‐hydroxylating oxygenases in the management of bioremediation and biocatalysis of aromatic compounds
Author(s) -
Chakraborty Joydeep,
Jana Tanmoy,
Saha Sudipto,
Dutta Tapan K.
Publication year - 2014
Publication title -
environmental microbiology reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.229
H-Index - 69
ISSN - 1758-2229
DOI - 10.1111/1758-2229.12182
Subject(s) - oxygenase , database , bioremediation , chemistry , computational biology , biology , bacteria , biochemistry , gene , computer science , genetics
Summary Bacterial R ieske‐type aromatic ring‐hydroxylating oxygenases ( RHO s) constitute a large family of enzymes, primarily involved in bioremediation of diverse aromatic compounds in the environment. In the present study, we have designed a manually curated database, R ing‐ H ydroxylating O xygenase database ( RHO base), which provides comprehensive information on all biochemically characterized bacterial RHO s. It consists of ∼ 1000 entries including 196 oxygenase α‐subunits, 153 oxygenase β‐subunits, 92 ferredoxins and 110 reductases, distributed among 131 different bacterial strains implementing a total of 318 oxygenation reactions. For each protein, users can get detailed information about its structure and conserved domain(s) with motif signature. RHO base allows users to search a query, based on organism, oxygenase, substrate, or protein structure. In addition, this resource provides analysis tools to perform blast search against RHO base for prediction of putative substrate(s) for the query oxygenase and its phylogenetic affiliation. Furthermore, there is an integrated cheminformatics tool to search for structurally similar compound(s) in the database vis‐a‐vis RHO (s) capable of transforming those compound(s). Resources in the RHO base and multiple search/display options therein are intended to provide oxygenase‐related requisite information to researchers, especially working in the field of environmental microbiology and biocatalysis to attain difficult chemistry of biotechnological importance.