spacer
spacer

PDBsum entry 1ps9

Go to PDB code: 
protein ligands metals links
Oxidoreductase PDB id
1ps9
Jmol
Contents
Protein chain
671 a.a. *
Ligands
SF4
FAD
FMN
NAP
MDE
Metals
_CL ×3
Waters ×373
* Residue conservation analysis
PDB id:
1ps9
Name: Oxidoreductase
Title: The crystal structure and reaction mechanism of e. Coli 2,4- dienoyl coa reductase
Structure: 2,4-dienoyl-coa reductase. Chain: a. Synonym: 2,4-dienoyl coenzyme a reductase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: fadh. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.203     R-free:   0.243
Authors: P.A.Hubbard,X.Liang,H.Schulz,J.J.Kim
Key ref:
P.A.Hubbard et al. (2003). The crystal structure and reaction mechanism of Escherichia coli 2,4-dienoyl-CoA reductase. J Biol Chem, 278, 37553-37560. PubMed id: 12840019 DOI: 10.1074/jbc.M304642200
Date:
20-Jun-03     Release date:   30-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P42593  (FADH_ECOLI) -  2,4-dienoyl-CoA reductase [NADPH]
Seq:
Struc:
 
Seq:
Struc:
672 a.a.
671 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.3.1.34  - 2,4-dienoyl-CoA reductase (NADPH).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Trans-2,3-didehydroacyl-CoA + NADP+ = trans,trans-2,3,4,5- tetradehydroacyl-CoA + NADPH
Trans-2,3-didehydroacyl-CoA
+
NADP(+)
Bound ligand (Het Group name = NAP)
corresponds exactly
=
trans,trans-2,3,4,5- tetradehydroacyl-CoA
Bound ligand (Het Group name = MDE)
matches with 84.00% similarity
+ NADPH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M304642200 J Biol Chem 278:37553-37560 (2003)
PubMed id: 12840019  
 
 
The crystal structure and reaction mechanism of Escherichia coli 2,4-dienoyl-CoA reductase.
P.A.Hubbard, X.Liang, H.Schulz, J.J.Kim.
 
  ABSTRACT  
 
Escherichia coli 2,4-dienoyl-CoA reductase is an iron-sulfur flavoenzyme required for the metabolism of unsaturated fatty acids with double bonds at even carbon positions. The enzyme contains FMN, FAD, and a 4Fe-4S cluster and exhibits sequence homology to another iron-sulfur flavoprotein, trimethylamine dehydrogenase. It also requires NADPH as an electron source, resulting in reduction of the C4-C5 double bond of the acyl chain of the CoA thioester substrate. The structure presented here of a ternary complex of E. coli 2,4-dienoyl-CoA reductase with NADP+ and a fatty acyl-CoA substrate reveals a possible mechanism for substrate reduction and provides details of a plausible electron transfer mechanism involving both flavins and the iron-sulfur cluster. The reaction is initiated by hydride transfer from NADPH to FAD, which in turn transfers electrons, one at a time, to FMN via the 4Fe-4S cluster. In the final stages of the reaction, the fully reduced FMN provides a hydride ion to the C5 atom of substrate, and Tyr-166 and His-252 are proposed to form a catalytic dyad that protonates the C4 atom of the substrate and complete the reaction. Inspection of the substrate binding pocket explains the relative promiscuity of the enzyme, catalyzing reduction of both 2-trans,4-cis- and 2-trans,4-trans-dienoyl-CoA thioesters.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Ribbon diagram outlining the overall fold of E. coli DCR. The N-terminal TIM barrel is red, with the substrate in yellow balls-and-sticks and FMN in pink balls-and-sticks. The 4Fe-4S cluster is in the center of the figure. The middle flavodoxin-like domain is in green, with FAD drawn as green balls-and-sticks. The C-terminal domain is in blue and includes NADP(H) as blue balls-and-sticks. For clarity, the N and C termini are denoted with the letters N and C, respectively.
Figure 6.
FIG. 6. Proposed reaction mechanism of E. coli DCR. I, the C5 atom of the acyl chain of substrate undergoes nucleophilic attack by the hydride ion from the N5 atom of fully reduced FMN. Glu-164 and a water molecule (WAT[2]) form hydrogen bonds to the thioester carbonyl oxygen of substrate, stabilizing the enolate form of substrate, and the C5 atom is primed for nucleophilic attack. A water molecule (WAT[1]) acts as a general base to deprotonate the N1 atom of FMN during flavin oxidation. II, Tyr-166 provides a proton to the C4 carbanion of substrate, completing reduction of the C4-C5 double bond. III, His-252 acts to stabilize the phenolate intermediate by providing a hydrogen bond to Tyr-166.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 37553-37560) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20824208 J.T.Noel, N.Arrach, A.Alagely, M.McClelland, and M.Teplitski (2010).
Specific responses of Salmonella enterica to tomato varieties and fruit ripeness identified by in vivo expression technology.
  PLoS One, 5, e12406.  
18047844 D.J.Kang, J.M.Ridlon, D.R.Moore, S.Barnes, and P.B.Hylemon (2008).
Clostridium scindens baiCD and baiH genes encode stereo-specific 7alpha/7beta-hydroxy-3-oxo-delta4-cholenoic acid oxidoreductases.
  Biochim Biophys Acta, 1781, 16-25.  
15103152 A.M.Orville, L.Manning, D.S.Blehert, J.M.Studts, B.G.Fox, and G.H.Chambliss (2004).
Crystallization and preliminary analysis of xenobiotic reductase A and ligand complexes from Pseudomonas putida II-B.
  Acta Crystallogr D Biol Crystallogr, 60, 957-961.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.