DB code: S00526

RLCP classification 8.11113.45000.86 : Isomerization
1.51.3100.78 : Hydrolysis
8.11131.365050.86 : Isomerization
CATH domain 3.40.50.1820 : Rossmann fold Catalytic domain
E.C. 3.7.1.-
CSA 1uk7
M-CSA 1uk7
MACiE

CATH domain Related DB codes (homologues)
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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P96965
2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
PF00561 (Abhydrolase_1)
[Graphical View]

KEGG enzyme name

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P96965 P96965_PSEFL

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C06582 C00001 C02632 C00596
E.C.
Compound 2-Hydroxy-6-oxo-7-methylocta-2,4-dienoate H2O 2-Methylpropanoate 2-Oxopent-4-enoate
Type carbohydrate,carboxyl group H2O carboxyl group carbohydrate,carboxyl group
ChEBI 83171
15377
16135
1113
PubChem 5280967
22247451
962
6590
5280361
1iunA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1iunB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1iuoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT_300 Unbound
1iupA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:ALQ_1300 Unbound
1uk6A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:PPI_1300 Unbound
1uk7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:BUA_1300 Unbound
1uk8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:LEA_1300 Unbound
1uk9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:IVA_1300 Unbound
1ukaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SMB_1300 Unbound
1ukbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:BEZ_1300 Unbound

Reference for Active-site residues
resource references E.C.
literature [10], [13]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1iunA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 224;HIS 252 mutant S103A
1iunB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 224;HIS 252 mutant S103A
1iuoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 224;HIS 252 mutant S103A
1iupA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 224;HIS 252 mutant S103A
1uk6A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 224;HIS 252 mutant S103A
1uk7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 224;HIS 252 mutant S103A
1uk8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 224;HIS 252 mutant S103A
1uk9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 224;HIS 252 mutant S103A
1ukaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 224;HIS 252 mutant S103A
1ukbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 224;HIS 252 mutant S103A

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 8449871
Journal J Bacteriol
Year 1993
Volume 175
Pages 1621-8
Authors Kohler HP, Schmid A, van der Maarel M
Title Metabolism of 2,2'-dihydroxybiphenyl by Pseudomonas sp. strain HBP1: production and consumption of 2,2',3-trihydroxybiphenyl.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 7890778
Journal J Biol Chem
Year 1995
Volume 270
Pages 6403-411
Authors Diaz E, Timmis KN
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.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID
Journal Proc Jpn Acad Ser B
Year 1997
Volume 73
Pages 154
Authors Nandhagopal N, Senda T, Hatta T, Yamada A, Masai E, Fukuda M, Mitsui Y
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.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9722515
Journal J Biol Chem
Year 1998
Volume 273
Pages 22943-9
Authors Seah SY, Terracina G, Bolin JT, Riebel P, Snieckus V, Eltis LD
Title Purification and preliminary characterization of a serine hydrolase involved in the microbial degradation of polychlorinated biphenyls.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10684634
Journal Biochemistry
Year 2000
Volume 39
Pages 1522-31
Authors Fleming SM, Robertson TA, Langley GJ, Bugg TD
Title Catalytic mechanism of a C-C hydrolase enzyme: evidence for a gem-diol intermediate, not an acyl enzyme.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 12369917
Journal Curr Protein Pept Sci
Year 2000
Volume 1
Pages 209-35
Authors Holmquist M
Title Alpha/Beta-hydrolase fold enzymes: structures, functions and mechanisms.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 10821847
Journal J Biol Chem
Year 2000
Volume 275
Pages 15701-8
Authors Seah SY, Labbe G, Nerdinger S, Johnson MR, Snieckus V, Eltis LD
Title Identification of a serine hydrolase as a key determinant in the microbial degradation of polychlorinated biphenyls.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11399084
Journal J Mol Biol
Year 2001
Volume 309
Pages 1139-1151
Authors Nandhagopal N, Yamada A, Hatta T, Masai E, Fukuda M, Mitsui Y, Senda T
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.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 12418219
Journal Methods Enzymol
Year 2002
Volume 354
Pages 106-18
Authors Bugg TD, Fleming SM, Robertson TA, Langley GJ
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.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 12192074
Journal Protein Sci
Year 2002
Volume 11
Pages 2184-95
Authors Fushinobu S, Saku T, Hidaka M, Jun SY, Nojiri H, Yamane H, Shoun H, Omori T, Wakagi T
Title Crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products.
Related PDB 1iun 1iuo 1iup
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 12659866
Journal Biochem Biophys Res Commun
Year 2003
Volume 303
Pages 631-9
Authors Habe H, Morii K, Fushinobu S, Nam JW, Ayabe Y, Yoshida T, Wakagi T, Yamane H, Nojiri H, Omori T
Title Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme).
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 12619671
Journal Biosci Biotechnol Biochem
Year 2003
Volume 67
Pages 36-45
Authors Nojiri H, Taira H, Iwata K, Morii K, Nam JW, Yoshida T, Habe H, Nakamura S, Shimizu K, Yamane H, Omori T
Title Purification and characterization of meta-cleavage compound hydrolase from a carbazole degrader Pseudomonas resinovorans strain CA10.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 15784976
Journal Biosci Biotechnol Biochem
Year 2005
Volume 69
Pages 491-8
Authors Fushinobu S, Jun SY, Hidaka M, Nojiri H, Yamane H, Shoun H, Omori T, Wakagi T
Title A series of crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with various cleavage products.
Related PDB 1uk6 1uk7 1uk8 1uk9 1uka 1ukb
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 15663941
Journal J Mol Biol
Year 2005
Volume 346
Pages 241-51
Authors Li C, Montgomery MG, Mohammed F, Li JJ, Wood SP, Bugg TD
Title Catalytic mechanism of C-C hydrolase MhpC from Escherichia coli: kinetic analysis of His263 and Ser110 site-directed mutants.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 15663942
Journal J Mol Biol
Year 2005
Volume 346
Pages 253-65
Authors Dunn G, Montgomery MG, Mohammed F, Coker A, Cooper JB, Robertson T, Garcia JL, Bugg TD, Wood SP
Title The structure of the C-C bond hydrolase MhpC provides insights into its catalytic mechanism.
Related PDB 1u2e
Related UniProtKB

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.

Created Updated
2003-07-28 2009-03-16