EzCatDB: S00526

DB codeS00526
RLCP classification8.11113.45000.86
1.51.3100.78
8.11131.365050.86
CATH domainDomain 13.40.50.1820Catalytic domain
E.C.3.7.1.-
CSA1uk7

CATH domainRelated DB codes (homologues)
3.40.50.1820S00544,S00344,S00517,S00525,S00720,S00723,S00724,S00725,S00919,S00057,S00374,S00345,S00347,S00348,S00346,S00350,S00352,S00353,S00355,S00356,S00358,D00189,D00210,D00539,T00253

Enzyme Name
Swiss-prot

P96965
Protein name
Synonyms2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase


Swiss-prot:Accession NumberP96965
Entry nameP96965_PSEFL
Activity
Subunit
Subcellular location
Cofactor


SubstratesProducts
KEGG-idC06582C00001C02632C00596
Compound2-Hydroxy-6-oxo-7-methylocta-2,4-dienoateH2O2-Methylpropanoate2-Oxopent-4-enoate
Typecarbohydrate,carboxyl groupH2Ocarboxyl groupcarbohydrate,carboxyl group
1iunAUnbound
UnboundUnbound
1iunBUnbound
UnboundUnbound
1iuoAUnbound
Analogue:ACT 300Unbound
1iupAUnbound
Bound:ALQ 1300Unbound
1uk6AUnbound
Analogue:PPI 1300Unbound
1uk7AUnbound
Analogue:BUA 1300Unbound
1uk8AUnbound
Analogue:LEA 1300Unbound
1uk9AUnbound
Analogue:IVA 1300Unbound
1ukaAUnbound
Analogue:SMB 1300Unbound
1ukbAUnbound
Analogue:BEZ 1300Unbound

Active-site residues
resource
literature [10], [13]
pdbCatalytic residuescomment
1iunA       ;ASP 224;HIS 252
mutant S103A
1iunB       ;ASP 224;HIS 252
mutant S103A
1iuoA       ;ASP 224;HIS 252
mutant S103A
1iupA       ;ASP 224;HIS 252
mutant S103A
1uk6A       ;ASP 224;HIS 252
mutant S103A
1uk7A       ;ASP 224;HIS 252
mutant S103A
1uk8A       ;ASP 224;HIS 252
mutant S103A
1uk9A       ;ASP 224;HIS 252
mutant S103A
1ukaA       ;ASP 224;HIS 252
mutant S103A
1ukbA       ;ASP 224;HIS 252
mutant S103A

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[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

references
[1]
PubMed ID8449871
JournalJ Bacteriol
Year1993
Volume175
Pages1621-8
AuthorsKohler HP, Schmid A, van der Maarel M
TitleMetabolism of 2,2'-dihydroxybiphenyl by Pseudomonas sp. strain HBP1: production and consumption of 2,2',3-trihydroxybiphenyl.
[2]
PubMed ID7890778
JournalJ Biol Chem
Year1995
Volume270
Pages6403-411
AuthorsDiaz E, Timmis KN
TitleIdentification 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.
[3]
JournalProc Jpn Acad Ser B
Year1997
Volume73
Pages154
AuthorsNandhagopal N, Senda T, Hatta T, Yamada A, Masai E, Fukuda M, Mitsui Y
TitleThree-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.
[4]
PubMed ID9722515
JournalJ Biol Chem
Year1998
Volume273
Pages22943-9
AuthorsSeah SY, Terracina G, Bolin JT, Riebel P, Snieckus V, Eltis LD
TitlePurification and preliminary characterization of a serine hydrolase involved in the microbial degradation of polychlorinated biphenyls.
[5]
PubMed ID10684634
JournalBiochemistry
Year2000
Volume39
Pages1522-31
AuthorsFleming SM, Robertson TA, Langley GJ, Bugg TD
TitleCatalytic mechanism of a C-C hydrolase enzyme: evidence for a gem-diol intermediate, not an acyl enzyme.
[6]
PubMed ID12369917
JournalCurr Protein Pept Sci
Year2000
Volume1
Pages209-35
AuthorsHolmquist M
TitleAlpha/Beta-hydrolase fold enzymes: structures, functions and mechanisms.
[7]
PubMed ID10821847
JournalJ Biol Chem
Year2000
Volume275
Pages15701-8
AuthorsSeah SY, Labbe G, Nerdinger S, Johnson MR, Snieckus V, Eltis LD
TitleIdentification of a serine hydrolase as a key determinant in the microbial degradation of polychlorinated biphenyls.
[8]
PubMed ID11399084
JournalJ Mol Biol
Year2001
Volume309
Pages1139-1151
AuthorsNandhagopal N, Yamada A, Hatta T, Masai E, Fukuda M, Mitsui Y, Senda T
TitleCrystal 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.
[9]
PubMed ID12418219
JournalMethods Enzymol
Year2002
Volume354
Pages106-18
AuthorsBugg TD, Fleming SM, Robertson TA, Langley GJ
Title2-hydroxy-6-keto-nona-2,4-diene 1,9-dioic acid 5,6-hydrolase: evidence from 18O isotope exchange for gem-diol intermediate.
[10]
CommentsX-ray crystallography
PubMed ID12192074
JournalProtein Sci
Year2002
Volume11
Pages2184-95
AuthorsFushinobu S, Saku T, Hidaka M, Jun SY, Nojiri H, Yamane H, Shoun H, Omori T, Wakagi T
TitleCrystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products.
Related PDB1iun,1iuo,1iup
[11]
PubMed ID12659866
JournalBiochem Biophys Res Commun
Year2003
Volume303
Pages631-9
AuthorsHabe H, Morii K, Fushinobu S, Nam JW, Ayabe Y, Yoshida T, Wakagi T, Yamane H, Nojiri H, Omori T
TitleCrystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme).
[12]
PubMed ID12619671
JournalBiosci Biotechnol Biochem
Year2003
Volume67
Pages36-45
AuthorsNojiri H, Taira H, Iwata K, Morii K, Nam JW, Yoshida T, Habe H, Nakamura S, Shimizu K, Yamane H, Omori T
TitlePurification and characterization of meta-cleavage compound hydrolase from a carbazole degrader Pseudomonas resinovorans strain CA10.
[13]
CommentsX-ray crystallography
PubMed ID15784976
JournalBiosci Biotechnol Biochem
Year2005
Volume69
Pages491-8
AuthorsFushinobu S, Jun SY, Hidaka M, Nojiri H, Yamane H, Shoun H, Omori T, Wakagi T
TitleA series of crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with various cleavage products.
Related PDB1uk6,1uk7,1uk8,1uk9,1uka,1ukb
[14]
PubMed ID15663941
JournalJ Mol Biol
Year2005
Volume346
Pages241-51
AuthorsLi C, Montgomery MG, Mohammed F, Li JJ, Wood SP, Bugg TD
TitleCatalytic mechanism of C-C hydrolase MhpC from Escherichia coli: kinetic analysis of His263 and Ser110 site-directed mutants.
[15]
PubMed ID15663942
JournalJ Mol Biol
Year2005
Volume346
Pages253-65
AuthorsDunn G, Montgomery MG, Mohammed F, Coker A, Cooper JB, Robertson T, Garcia JL, Bugg TD, Wood SP
TitleThe structure of the C-C bond hydrolase MhpC provides insights into its catalytic mechanism.
Related PDB1u2e

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.

createdupdated
2003-07-282009-03-16


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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