EzCatDB: S00849
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DB codeS00849
RLCP classification8.131.161950.140 : Isomerization
8.11113.362040.140 : Isomerization
CATH domainDomain 13.90.226.10 : 2-enoyl-CoA Hydratase; Chain A, domain 1Catalytic domain
E.C.5.3.3.8
CSA1pjh

CATH domainRelated DB codes (homologues)
3.90.226.10 : 2-enoyl-CoA Hydratase; Chain A, domain 1M00145,M00122,D00254

Enzyme Name
UniProtKBKEGG

Q05871
Protein name3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) (Dodecenoyl-CoA isomerase) (DeltaDodecenoyl-CoA isomerase
Dodecenoyl-CoA Delta-isomerase
Delta3-cis-Delta2-trans-enoyl-CoA isomerase
Acetylene-allene isomerase
Dodecenoyl-CoA Delta-isomerase
Dodecenoyl-CoA Delta3-cis-Delta2-trans-isomerase
Synonyms3),Delta(2)-enoyl-CoA isomerase
D3,D2-enoyl-CoA isomerase
RefSeqNP_013386.1 (Protein)
NM_001182171.1 (DNA/RNA sequence)
PfamPF00378 (ECH)
[Graphical view]


UniProtKB:Accession NumberQ05871
Entry nameECI1_YEAST
Activity(3Z)-Dodec-3-enoyl-CoA = (2E)-dodec-2-enoyl-CoA.
SubunitHomohexamer. Interacts with DCI1.
Subcellular locationPeroxisome. This location is DCI1 dependent.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC02944C03221
Compound(3Z)-Dodec-3-enoyl-CoA(2E)-Dodec-2-enoyl-CoA
Typeamine group,carbohydrate,lipid,nucleotide,peptide/protein,sulfide groupamine group,carbohydrate,lipid,nucleotide,peptide/protein,sulfide group
ChEBI27989
15471
PubChem5280554
11966217
5280578
11966110
          
1hnoA00UnboundUnbound
1hnuA00UnboundUnbound
1k39A00Analogue:CO8Unbound
1k39B00Analogue:CO8Unbound
1k39C00Analogue:CO8Unbound
1pjhA00UnboundUnbound
1pjhB00UnboundUnbound
1pjhC00UnboundUnbound

Active-site residues
resource
literature [3]
pdbCatalytic residuesMain-chain involved in catalysis
          
1hnoA00GLU 158
ALA 70;LEU 126
1hnuA00GLU 158
ALA 70;LEU 126
1k39A00GLU 158
ALA 70;LEU 126
1k39B00GLU 158
ALA 70;LEU 126
1k39C00GLU 158
ALA 70;LEU 126
1pjhA00GLU 158
ALA 70;LEU 126
1pjhB00GLU 158
ALA 70;LEU 126
1pjhC00GLU 158
ALA 70;LEU 126

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]Figure 1, p.851
[8]Fig.4, p.2516

references
[1]
PubMed ID9813046
JournalJ Biol Chem
Year1998
Volume273
Pages31366-74
AuthorsGurvitz A, Mursula AM, Firzinger A, Hamilton B, Kilpelainen SH, Hartig A, Ruis H, Hiltunen JK, Rottensteiner H
TitlePeroxisomal Delta3-cis-Delta2-trans-enoyl-CoA isomerase encoded by ECI1 is required for growth of the yeast Saccharomyces cerevisiae on unsaturated fatty acids.
[2]
PubMed ID10944342
JournalActa Crystallogr D Biol Crystallogr
Year2000
Volume56
Pages1020-3
AuthorsMursula AM, van Aalten DM, Modis Y, Hiltunen JK, Wierenga RK
TitleCrystallization and X-ray diffraction analysis of peroxisomal Delta3-Delta2-enoyl-CoA isomerase from Saccharomyces cerevisiae.
Related UniProtKBQ05871
[3]
PubMed ID11399063
JournalJ Mol Biol
Year2001
Volume309
Pages845-53
AuthorsMursula AM, van Aalten DM, Hiltunen JK, Wierenga RK
TitleThe crystal structure of delta(3)-delta(2)-enoyl-CoA isomerase.
Related PDB1hno,1hnu
Related UniProtKBQ05871
[4]
PubMed ID11781327
JournalJ Biol Chem
Year2002
Volume277
Pages9127-32
AuthorsZhang D, Yu W, Geisbrecht BV, Gould SJ, Sprecher H, Schulz H
TitleFunctional characterization of Delta3,Delta2-enoyl-CoA isomerases from rat liver.
[5]
PubMed ID14741345
JournalFEBS Lett
Year2004
Volume557
Pages81-7
AuthorsMursula AM, Hiltunen JK, Wierenga RK
TitleStructural studies on delta(3)-delta(2)-enoyl-CoA isomerase: the variable mode of assembly of the trimeric disks of the crotonase superfamily.
Related PDB1pjh
Related UniProtKBQ05871
[6]
PubMed ID15351645
JournalJ Mol Biol
Year2004
Volume342
Pages1197-208
AuthorsPartanen ST, Novikov DK, Popov AN, Mursula AM, Hiltunen JK, Wierenga RK
TitleThe 1.3 A crystal structure of human mitochondrial Delta3-Delta2-enoyl-CoA isomerase shows a novel mode of binding for the fatty acyl group.
[7]
PubMed ID17028011
JournalBiochim Biophys Acta
Year2006
Volume1763
Pages1413-26
AuthorsPoirier Y, Antonenkov VD, Glumoff T, Hiltunen JK
TitlePeroxisomal beta-oxidation--a metabolic pathway with multiple functions.
[8]
PubMed ID18470480
JournalCell Mol Life Sci
Year2008
Volume65
Pages2507-27
AuthorsHamed RB, Batchelar ET, Clifton IJ, Schofield CJ
TitleMechanisms and structures of crotonase superfamily enzymes--how nature controls enolate and oxyanion reactivity.

comments
This enzyme belongs to 2-enoyl-CoA hydratase superfamily.
According to the literature [3] and [8], this enzyme catalyzes the following reactions:
(A) Isomerization from (3Z)-Dodec-3-enoyl-CoA to an enol intermediate:
(A1) Glu158 acts as a general base to deprotonate the C2 atom, giving a negatively charged thioester oxygen atom.
(A2) The negatively charged oxygen atom is stabilized by mainchain amide groups of Ala70 and Leu126.
(B) Isomerization from the enol intermediate to (2E)-Dodec-2-enoyl-CoA:
(B0) The negative charge on the thioester is stabilized by mainchain amide groups of Ala70 and Leu126.
(B1) Glu158 acts as a general acid to protonate the C4 atom, forming the thioester group again.

createdupdated
2009-10-092011-11-09


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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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