DB code: S00849

RLCP classification 8.131.161950.140 : Isomerization
8.11113.362040.140 : Isomerization
CATH domain 3.90.226.10 : 2-enoyl-CoA Hydratase; Chain A, domain 1 Catalytic domain
E.C. 5.3.3.8
CSA 1pjh
M-CSA 1pjh
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q05871 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) (Dodecenoyl-CoA isomerase) (Delta
3),Delta(2)-enoyl-CoA isomerase
D3,D2-enoyl-CoA isomerase
NP_013386.1 (Protein)
NM_001182171.1 (DNA/RNA sequence)
PF00378 (ECH)
[Graphical View]

KEGG enzyme name
Dodecenoyl-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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q05871 ECI1_YEAST (3Z)-Dodec-3-enoyl-CoA = (2E)-dodec-2-enoyl-CoA. Homohexamer. Interacts with DCI1. Peroxisome. This location is DCI1 dependent.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C02944 C03221
E.C.
Compound (3Z)-Dodec-3-enoyl-CoA (2E)-Dodec-2-enoyl-CoA
Type amine group,carbohydrate,lipid,nucleotide ,peptide/protein,sulfide group amine group,carbohydrate,lipid,nucleotide ,peptide/protein,sulfide group
ChEBI 27989
15471
PubChem 11966217
5280554
11966110
5280578
1hnoA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1hnuA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1k39A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CO8 Unbound
1k39B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CO8 Unbound
1k39C00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CO8 Unbound
1pjhA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1pjhB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1pjhC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [3]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1hnoA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 158 ALA 70;LEU 126
1hnuA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 158 ALA 70;LEU 126
1k39A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 158 ALA 70;LEU 126
1k39B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 158 ALA 70;LEU 126
1k39C00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 158 ALA 70;LEU 126
1pjhA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 158 ALA 70;LEU 126
1pjhB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 158 ALA 70;LEU 126
1pjhC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 158 ALA 70;LEU 126

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
Figure 1, p.851
[8]
Fig.4, p.2516

References
[1]
Resource
Comments
Medline ID
PubMed ID 9813046
Journal J Biol Chem
Year 1998
Volume 273
Pages 31366-74
Authors Gurvitz A, Mursula AM, Firzinger A, Hamilton B, Kilpelainen SH, Hartig A, Ruis H, Hiltunen JK, Rottensteiner H
Title Peroxisomal Delta3-cis-Delta2-trans-enoyl-CoA isomerase encoded by ECI1 is required for growth of the yeast Saccharomyces cerevisiae on unsaturated fatty acids.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 10944342
Journal Acta Crystallogr D Biol Crystallogr
Year 2000
Volume 56
Pages 1020-3
Authors Mursula AM, van Aalten DM, Modis Y, Hiltunen JK, Wierenga RK
Title Crystallization and X-ray diffraction analysis of peroxisomal Delta3-Delta2-enoyl-CoA isomerase from Saccharomyces cerevisiae.
Related PDB
Related UniProtKB Q05871
[3]
Resource
Comments
Medline ID
PubMed ID 11399063
Journal J Mol Biol
Year 2001
Volume 309
Pages 845-53
Authors Mursula AM, van Aalten DM, Hiltunen JK, Wierenga RK
Title The crystal structure of delta(3)-delta(2)-enoyl-CoA isomerase.
Related PDB 1hno 1hnu
Related UniProtKB Q05871
[4]
Resource
Comments
Medline ID
PubMed ID 11781327
Journal J Biol Chem
Year 2002
Volume 277
Pages 9127-32
Authors Zhang D, Yu W, Geisbrecht BV, Gould SJ, Sprecher H, Schulz H
Title Functional characterization of Delta3,Delta2-enoyl-CoA isomerases from rat liver.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 14741345
Journal FEBS Lett
Year 2004
Volume 557
Pages 81-7
Authors Mursula AM, Hiltunen JK, Wierenga RK
Title Structural studies on delta(3)-delta(2)-enoyl-CoA isomerase: the variable mode of assembly of the trimeric disks of the crotonase superfamily.
Related PDB 1pjh
Related UniProtKB Q05871
[6]
Resource
Comments
Medline ID
PubMed ID 15351645
Journal J Mol Biol
Year 2004
Volume 342
Pages 1197-208
Authors Partanen ST, Novikov DK, Popov AN, Mursula AM, Hiltunen JK, Wierenga RK
Title The 1.3 A crystal structure of human mitochondrial Delta3-Delta2-enoyl-CoA isomerase shows a novel mode of binding for the fatty acyl group.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 17028011
Journal Biochim Biophys Acta
Year 2006
Volume 1763
Pages 1413-26
Authors Poirier Y, Antonenkov VD, Glumoff T, Hiltunen JK
Title Peroxisomal beta-oxidation--a metabolic pathway with multiple functions.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 18470480
Journal Cell Mol Life Sci
Year 2008
Volume 65
Pages 2507-27
Authors Hamed RB, Batchelar ET, Clifton IJ, Schofield CJ
Title Mechanisms and structures of crotonase superfamily enzymes--how nature controls enolate and oxyanion reactivity.
Related PDB
Related UniProtKB

Comments
(B1) Glu158 acts as a general acid to protonate the C4 atom, forming the thioester group again.
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.

Created Updated
2009-10-09 2011-11-09