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PDBsum entry 1sg4

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1sg4
Jmol
Contents
Protein chain
249 a.a. *
Ligands
CO8
Waters ×667
* Residue conservation analysis
PDB id:
1sg4
Name: Isomerase
Title: Crystal structure of human mitochondrial delta3-delta2- enoyl-coa isomerase
Structure: 3,2-trans-enoyl-coa isomerase, mitochondrial. Chain: a, b, c. Synonym: dodecenoyl-coa delta-isomerase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: dci. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.30Å     R-factor:   0.157     R-free:   0.202
Authors: S.T.Partanen,D.K.Novikov,A.N.Popov,A.M.Mursula,J.K.Hiltunen, R.K.Wierenga
Key ref:
S.T.Partanen et al. (2004). 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. J Mol Biol, 342, 1197-1208. PubMed id: 15351645 DOI: 10.1016/j.jmb.2004.07.039
Date:
23-Feb-04     Release date:   18-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P42126  (ECI1_HUMAN) -  Enoyl-CoA delta isomerase 1, mitochondrial
Seq:
Struc:
302 a.a.
249 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.3.3.8  - Dodecenoyl-CoA isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (3Z)-dodec-3-enoyl-CoA = (2E)-dodec-2-enoyl-CoA
(3Z)-dodec-3-enoyl-CoA
Bound ligand (Het Group name = CO8)
matches with 93.00% similarity
= (2E)-dodec-2-enoyl-CoA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     1 term  

 

 
    Added reference    
 
 
DOI no: 10.1016/j.jmb.2004.07.039 J Mol Biol 342:1197-1208 (2004)
PubMed id: 15351645  
 
 
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.
S.T.Partanen, D.K.Novikov, A.N.Popov, A.M.Mursula, J.K.Hiltunen, R.K.Wierenga.
 
  ABSTRACT  
 
The crystal structure of Delta3-Delta2-enoyl-CoA isomerase from human mitochondria (hmEci), complexed with the substrate analogue octanoyl-CoA, has been refined at 1.3 A resolution. This enzyme takes part in the beta-oxidation of unsaturated fatty acids by converting both cis-3 and trans-3-enoyl-CoA esters (with variable length of the acyl group) to trans-2-enoyl-CoA. hmEci belongs to the hydratase/isomerase (crotonase) superfamily. Most of the enzymes belonging to this superfamily are hexamers, but hmEci is shown to be a trimer. The mode of binding of the ligand, octanoyl-CoA, shows that the omega-end of the acyl group binds in a hydrophobic tunnel formed by residues of the loop preceding helix H4 as well as by side-chains of the kinked helix H9. From the structure of the complex it can be seen that Glu136 is the only catalytic residue. The importance of Glu136 for catalysis is confirmed by mutagenesis studies. A cavity analysis shows the presence of two large, adjacent empty hydrophobic cavities near the active site, which are shaped by side-chains of helices H1, H2, H3 and H4. The structure comparison of hmEci with structures of other superfamily members, in particular of rat mitochondrial hydratase (crotonase) and yeast peroxisomal enoyl-CoA isomerase, highlights the variable mode of binding of the fatty acid moiety in this superfamily.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The reaction catalyzed by the isomerase. It is known that substrate can be either cis-3 or trans-3, but it is currently not known if the cis-3 and trans-3 fatty acid tails bind in the same binding pocket.
Figure 5.
Figure 5. Comparison of the unliganded subunit (subunit A; red) and liganded subunit (subunit B; green). For the liganded subunit, only the octanoyl-CoA (orange) and the regions of structural difference (near H2, H9 and H10) are shown.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 1197-1208) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21308811 I.Pápai, A.Hamza, P.M.Pihko, and R.K.Wierenga (2011).
Stereoelectronic requirements for optimal hydrogen-bond-catalyzed enolization.
  Chemistry, 17, 2859-2866.  
20826346 Z.Cheng, Y.W.He, S.C.Lim, R.Qamra, M.A.Walsh, L.H.Zhang, and H.Song (2010).
Structural basis of the sensor-synthase interaction in autoinduction of the quorum sensing signal DSF biosynthesis.
  Structure, 18, 1199-1209.
PDB codes: 3m6m 3m6n
19369256 J.Bains, R.Leon, and M.J.Boulanger (2009).
Structural and Biophysical Characterization of BoxC from Burkholderia xenovorans LB400: A NOVEL RING-CLEAVING ENZYME IN THE CROTONASE SUPERFAMILY.
  J Biol Chem, 284, 16377-16385.
PDB code: 2w3p
18657232 S.Goepfert, C.Vidoudez, C.Tellgren-Roth, S.Delessert, J.K.Hiltunen, and Y.Poirier (2008).
Peroxisomal Delta(3),Delta(2)-enoyl CoA isomerases and evolution of cytosolic paralogues in embryophytes.
  Plant J, 56, 728-742.  
17928301 T.W.Geders, L.Gu, J.C.Mowers, H.Liu, W.H.Gerwick, K.Håkansson, D.H.Sherman, and J.L.Smith (2007).
Crystal structure of the ECH2 catalytic domain of CurF from Lyngbya majuscula. Insights into a decarboxylase involved in polyketide chain beta-branching.
  J Biol Chem, 282, 35954-35963.
PDB codes: 2q2x 2q34 2q35
16889958 V.Z.Pletnev, J.L.Thomas, F.L.Rhaney, L.S.Holt, L.A.Scaccia, T.C.Umland, and W.L.Duax (2006).
Rational proteomics V: structure-based mutagenesis has revealed key residues responsible for substrate recognition and catalysis by the dehydrogenase and isomerase activities in human 3beta-hydroxysteroid dehydrogenase/isomerase type 1.
  J Steroid Biochem Mol Biol, 101, 50-60.  
15883186 P.A.Hubbard, W.Yu, H.Schulz, and J.J.Kim (2005).
Domain swapping in the low-similarity isomerase/hydratase superfamily: the crystal structure of rat mitochondrial Delta3, Delta2-enoyl-CoA isomerase.
  Protein Sci, 14, 1545-1555.
PDB code: 1xx4
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.