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Overview for MACiE Entry M0108

Version history

General Information

EC Number: 1.3.1.34 (A member of the Oxidoreductases, Acting on the CH-CH group of donors, With NAD+ or NADP+ as acceptor)

Enzyme Name: 2,4-dienoyl-CoA reductase (NADPH)

Biological Species: Escherichia coli (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P42593 - 2,4-dienoyl-CoA reductase [NADPH]

Representative PDB Code: 1ps9 - THE CRYSTAL STRUCTURE AND REACTION MECHANISM OF E. COLI 2,4-DIENOYL COA REDUCTASE (Resolution = 2.20 Å).

Catalytic CATH Codes:

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of NADPH

Image of trans,trans-2,3,4,5-tetradehydroacyl-CoA

Image of proton

right arrow

Image of NADP

Image of trans-2,3-didehydroacyl-CoA

NADPH
C00005
CHEBI:16474
trans,trans-2,3,4,5-tetradehydroacyl-CoA
C04512
CHEBI:58036
proton
C00080
CHEBI:24636
NADP
C00006
CHEBI:18009
trans-2,3-didehydroacyl-CoA
C00658
CHEBI:58856

Overall Comment: This enzyme is unusual in that it lacks stereospecificity, catalysing the reduction of both natural fatty acids with cis double bonds, as well as substrates containing trans double bonds, this might be explained by the large size of the substrate binding pocket [1].


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Stepwise Description of the Reaction

Step 1NADP eliminates a hydride ion, which is added to FAD.
Step 2FAD transfers a single electron, through Gln339 and an iron-sulfur cluster, to FMN, which deprotonates water.
Step 3Water deprotonates FAD, which initiates a second single electron transfer, through Gln339 and an iron-sulfur cluster, to FMN. This regenerates the FAD cofactor, and produces fully reduced FMN.
Step 4FMN eliminates a hydride ion, which is added to the C5 of the substrate. This initiates double bond rearrangement, resulting in an oxyanion on the C1.
Step 5The oxyanion collapses, initiating double bond rearrangement, the C4 of the intermediate deprotonates Tyr166.
Step 6Tyr166 deprotonates water in an inferred return step.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Glu 164 A Side Chain
Tyr 166 A Side Chain
Arg 214 A Side Chain
His 252 A Side Chain
Gln 339 A Side Chain

Organic Cofactors for M0108

Type Identity Chain
FAD FAD 701 Overview
FMN FMN 702 Overview

Metal Cofactors for M0108

Type Het group Number Chain
iron FS4 700 A Overview

References

  1. P. A. Hubbard et al. (2003), J. Biol. Chem., 278, 37553-37560. The crystal structure and reaction mechanism of Escherichia coli 2,4-dienoyl-CoA reductase.
    Medline: 12840019

Homologue information for M0108 (1ps9)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0102 L-lactate dehydrogenase (cytochrome)
1.1.2.3
1fcb 3.20.20.70
0.34250.3162Compare
M0109 dihydroorotate oxidase
1.3.3.1
1d3g 3.20.20.70
0.58330.0258Compare
M0111 glutamate synthase (ferredoxin)
1.4.7.1
1ofd 3.20.20.70
0.46070.2999Compare
M0114 trimethylamine dehydrogenase
1.5.8.2
2tmd 3.20.20.70
3.50.50.60
3.40.50.720
0.380.3219Compare
M0319 NADPH dehydrogenase
1.6.99.1
1oya 3.20.20.70
0.50510.18Compare
M0148 transaldolase
2.2.1.2
1onr 3.20.20.70
0.28340.1232Compare
M0008 nicotinate-nucleotide diphosphorylase (carboxylating)
2.4.2.19
1qpr 3.20.20.70
0.13550.2571Compare
M0243 pyridoxine 5'-phosphate synthase
2.6.99.2
1ho1 3.20.20.70
0.46150.3803Compare
M0050 orotidine-5'-phosphate decarboxylase
4.1.1.23
1dbt 3.20.20.70
0.0350.0118Compare
M0252 indole-3-glycerol-phosphate synthase
4.1.1.48
1igs 3.20.20.70
0.30.1384Compare
M0236 3-dehydro-L-gulonate-6-phosphate decarboxylase
4.1.1.85
1q6l 3.20.20.70
0.22330.2645Compare
M0052 fructose-bisphosphate aldolase (Class II)
4.1.2.13
1b57 3.20.20.70
0.27110.1383Compare
M0222 fructose-bisphosphate aldolase (Class I)
4.1.2.13
2qut 3.20.20.70
0.24390.2200Compare
M0054 3-dehydroquinate dehydratase (type I)
4.2.1.10
1qfe 3.20.20.70
0.43380.2999Compare
M0230 porphobilinogen synthase
4.2.1.24
1gzg 3.20.20.70
0.48410Compare
M0267 dihydrodipicolinate synthase
4.2.1.52
1dhp 3.20.20.70
0.44260.1516Compare
M0270 ribulose-phosphate 3-epimerase
5.1.3.1
1h1z 3.20.20.70
0.21150.0165Compare
M0324 triosephosphate isomerase
5.3.1.1
1tph 3.20.20.70
0.22520.2571Compare
M0223 pyruvate carboxylase
6.4.1.1
2qf7 3.20.20.70
0.37770Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.20.20.70

View a comparison of the other reactions in MACiE with the CATH domain 3.40.50.720

View a comparison of the other reactions in MACiE with the CATH domain 3.50.50.60


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

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catalytic activity (molecular function)
metabolic process (biological process)
FMN binding (molecular function)
oxidoreductase activity (molecular function)
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