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CATH domain | Related DB codes (homologues) |
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3.40.50.1820 : Rossmann fold | S00544,S00344,S00517,S00525,S00720,S00723,S00724,S00725,S00919,S00057,S00374,S00345,S00347,S00348,S00346,S00350,S00352,S00353,S00355,S00356,S00358,D00189,D00210,D00539,T00253 |
UniProtKB:Accession Number | P96965 |
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Entry name | P96965_PSEFL |
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Activity |
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Subunit |
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Subcellular location |
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Cofactor |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[5] | Fig.6, p.1529-1530 |
| [6] | Fig.11, p.227-228 |
| [8] | p.1144-1147 |
| [9] | FIG.1, p.107 |
| [13] | p.495 |
| [14] | Fig.8, p.246-249 |
| [15] | Fig.1, p.261-262 |
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references | [1] |
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PubMed ID | 8449871 |
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Journal | J Bacteriol |
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Year | 1993 |
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Volume | 175 |
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Pages | 1621-8 |
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Authors | Kohler HP, Schmid A, van der Maarel M |
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Title | Metabolism of 2,2'-dihydroxybiphenyl by Pseudomonas sp. strain HBP1: production and consumption of 2,2',3-trihydroxybiphenyl. |
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[2] |
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PubMed ID | 7890778 |
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Journal | J Biol Chem |
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Year | 1995 |
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Volume | 270 |
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Pages | 6403-411 |
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Authors | Diaz E, Timmis KN |
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Title | Identification of functional residues in a 2-hydroxymuconic semialdehyde hydrolase. A new member of the alpha/beta hydrolase-fold family of enzymes which cleaves carbon-carbon bonds. |
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[3] |
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Journal | Proc Jpn Acad Ser B |
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Year | 1997 |
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Volume | 73 |
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Pages | 154 |
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Authors | Nandhagopal N, Senda T, Hatta T, Yamada A, Masai E, Fukuda M, Mitsui Y |
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Title | Three-dimensional structure of microbial 2-hydroxyl-6-oxo-6-phenylhexa-2,4- dienoic acid (hpda) hydrolase (bphd enzyme) from rhodococcussp. Strain rha1, in the pcb degradation pathway. |
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[4] |
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PubMed ID | 9722515 |
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Journal | J Biol Chem |
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Year | 1998 |
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Volume | 273 |
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Pages | 22943-9 |
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Authors | Seah SY, Terracina G, Bolin JT, Riebel P, Snieckus V, Eltis LD |
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Title | Purification and preliminary characterization of a serine hydrolase involved in the microbial degradation of polychlorinated biphenyls. |
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[5] |
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PubMed ID | 10684634 |
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Journal | Biochemistry |
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Year | 2000 |
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Volume | 39 |
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Pages | 1522-31 |
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Authors | Fleming SM, Robertson TA, Langley GJ, Bugg TD |
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Title | Catalytic mechanism of a C-C hydrolase enzyme: evidence for a gem-diol intermediate, not an acyl enzyme. |
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[6] |
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PubMed ID | 12369917 |
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Journal | Curr Protein Pept Sci |
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Year | 2000 |
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Volume | 1 |
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Pages | 209-35 |
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Authors | Holmquist M |
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Title | Alpha/Beta-hydrolase fold enzymes: structures, functions and mechanisms. |
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[7] |
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PubMed ID | 10821847 |
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Journal | J Biol Chem |
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Year | 2000 |
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Volume | 275 |
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Pages | 15701-8 |
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Authors | Seah SY, Labbe G, Nerdinger S, Johnson MR, Snieckus V, Eltis LD |
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Title | Identification of a serine hydrolase as a key determinant in the microbial degradation of polychlorinated biphenyls. |
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[8] |
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PubMed ID | 11399084 |
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Journal | J Mol Biol |
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Year | 2001 |
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Volume | 309 |
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Pages | 1139-1151 |
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Authors | Nandhagopal N, Yamada A, Hatta T, Masai E, Fukuda M, Mitsui Y, Senda T |
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Title | Crystal structure of 2-hydroxyl-6-oxo-6-phenylhexa-2,4-dienoic acid (HPDA) hydrolase (BphD enzyme) from the Rhodococcus sp. strain RHA1 of the PCB degradation pathway. |
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[9] |
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PubMed ID | 12418219 |
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Journal | Methods Enzymol |
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Year | 2002 |
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Volume | 354 |
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Pages | 106-18 |
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Authors | Bugg TD, Fleming SM, Robertson TA, Langley GJ |
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Title | 2-hydroxy-6-keto-nona-2,4-diene 1,9-dioic acid 5,6-hydrolase: evidence from 18O isotope exchange for gem-diol intermediate. |
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[10] |
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Comments | X-ray crystallography |
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PubMed ID | 12192074 |
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Journal | Protein Sci |
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Year | 2002 |
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Volume | 11 |
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Pages | 2184-95 |
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Authors | Fushinobu S, Saku T, Hidaka M, Jun SY, Nojiri H, Yamane H, Shoun H, Omori T, Wakagi T |
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Title | Crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products. |
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Related PDB | 1iun,1iuo,1iup |
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[11] |
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PubMed ID | 12659866 |
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Journal | Biochem Biophys Res Commun |
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Year | 2003 |
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Volume | 303 |
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Pages | 631-9 |
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Authors | Habe H, Morii K, Fushinobu S, Nam JW, Ayabe Y, Yoshida T, Wakagi T, Yamane H, Nojiri H, Omori T |
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Title | Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme). |
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[12] |
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PubMed ID | 12619671 |
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Journal | Biosci Biotechnol Biochem |
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Year | 2003 |
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Volume | 67 |
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Pages | 36-45 |
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Authors | Nojiri H, Taira H, Iwata K, Morii K, Nam JW, Yoshida T, Habe H, Nakamura S, Shimizu K, Yamane H, Omori T |
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Title | Purification and characterization of meta-cleavage compound hydrolase from a carbazole degrader Pseudomonas resinovorans strain CA10. |
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[13] |
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Comments | X-ray crystallography |
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PubMed ID | 15784976 |
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Journal | Biosci Biotechnol Biochem |
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Year | 2005 |
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Volume | 69 |
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Pages | 491-8 |
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Authors | Fushinobu S, Jun SY, Hidaka M, Nojiri H, Yamane H, Shoun H, Omori T, Wakagi T |
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Title | A series of crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with various cleavage products. |
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Related PDB | 1uk6,1uk7,1uk8,1uk9,1uka,1ukb |
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[14] |
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PubMed ID | 15663941 |
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Journal | J Mol Biol |
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Year | 2005 |
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Volume | 346 |
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Pages | 241-51 |
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Authors | Li C, Montgomery MG, Mohammed F, Li JJ, Wood SP, Bugg TD |
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Title | Catalytic mechanism of C-C hydrolase MhpC from Escherichia coli: kinetic analysis of His263 and Ser110 site-directed mutants. |
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[15] |
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PubMed ID | 15663942 |
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Journal | J Mol Biol |
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Year | 2005 |
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Volume | 346 |
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Pages | 253-65 |
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Authors | Dunn G, Montgomery MG, Mohammed F, Coker A, Cooper JB, Robertson T, Garcia JL, Bugg TD, Wood SP |
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Title | The structure of the C-C bond hydrolase MhpC provides insights into its catalytic mechanism. |
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Related PDB | 1u2e |
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comments | Although this enzyme has a catalytic triad composed of Ser/His/Asp, in which the catalytic serine acts as a nucleophile in double displacement mechanism for the other homologous enzymes, the literature [5], [9] & [10] proposed a different mechanism, which involves base-catalyzed attack of water rather than nucleophilic attack of the serine residue. Moreover, the other literature [6], [14] & [15] suggested that the hydrolysis reaction is coupled with ketonization of C2 carbon (keto-enol tautomerization or isomerization). According to the literature [14], the reactions of this enzyme proceed as follows: (A) Isomerization (shift od double-bond position): (A1) Asp224 modulates the activity of His252. (A2) His252 acts as a general base to deprotonate C2 hydroxyl group. (A3) His252 acts as a general acid to protonate C5 atom (protonation site) (B) Hydrolysis of carbonyl carbon-carbon bond: (B1) Asp224 modulates the activity of His252. (B2) His252 acts as a general base to activate water. This water is oriented by Ser103. (B3) The C6-ketone is twisted towards Ser103, so that it is positioned for the attack of the activated water. (B4) The activated water makes a nucleophilic attack on the C6-carbonyl carbon, leading to gem-diolate intermediate. The intermediate is stabilized by Ser103. (B5) The scissile C-C bond should be positioned parallel with the C=C pi bond. The cleavage of the scissile C-C bond occurs, accompanied by the following reaction. (C) Isomerization (shift od double-bond position): (C1) Asp224 modulates the activity of His252. (C2) His252 acts as a general acid to protonate C2 carbonyl oxygen.
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created | updated |
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2003-07-28 | 2009-03-16 |
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