PDBsum entry 1xx4

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Isomerase PDB id
Protein chain
254 a.a. *
PO4 ×3
BAM ×3
_ZN ×3
Waters ×90
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of rat mitochondrial 3,2-enoyl-coa
Structure: 3,2-trans-enoyl-coa isomerase, mitochondrial. Chain: a. Synonym: dodecenoyl-coa delta-isomerase. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: dci. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
2.20Å     R-factor:   0.239     R-free:   0.265
Authors: P.A.Hubbard,W.Yu,H.Schulz,J.-J.Kim
Key ref:
P.A.Hubbard et al. (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. PubMed id: 15883186 DOI: 10.1110/ps.041303705
03-Nov-04     Release date:   23-Nov-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P23965  (ECI1_RAT) -  Enoyl-CoA delta isomerase 1, mitochondrial
289 a.a.
254 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Dodecenoyl-CoA isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (3Z)-dodec-3-enoyl-CoA = (2E)-dodec-2-enoyl-CoA
= (2E)-dodec-2-enoyl-CoA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   2 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     4 terms  


    Added reference    
DOI no: 10.1110/ps.041303705 Protein Sci 14:1545-1555 (2005)
PubMed id: 15883186  
Domain swapping in the low-similarity isomerase/hydratase superfamily: the crystal structure of rat mitochondrial Delta3, Delta2-enoyl-CoA isomerase.
P.A.Hubbard, W.Yu, H.Schulz, J.J.Kim.
Two monofunctional Delta(3), Delta(2)-enoyl-CoA isomerases, one in mitochondria (mECI) and the other in both mitochondria and peroxisomes (pECI), belong to the low-similarity isomerase/hydratase superfamily. Both enzymes catalyze the movement of a double bond from C3 to C2 of an unsaturated acyl-CoA substrate for re-entry into the beta-oxidation pathway. Mutagenesis has shown that Glu165 of rat mECI is involved in catalysis; however, the putative catalytic residue in yeast pECI, Glu158, is not conserved in mECI. To elucidate whether Glu165 of mECI is correctly positioned for catalysis, the crystal structure of rat mECI has been solved. Crystal packing suggests the enzyme is trimeric, in contrast to other members of the superfamily, which appear crystallographically to be dimers of trimers. The polypeptide fold of mECI, like pECI, belongs to a subset of this superfamily in which the C-terminal domain of a given monomer interacts with its own N-terminal domain. This differs from that of crotonase and 1,4-dihydroxy-2-naphtoyl-CoA synthase, whose C-terminal domains are involved in domain swapping with an adjacent monomer. The structure confirms Glu165 as the putative catalytic acid/base, positioned to abstract the pro-R proton from C2 and reprotonate at C4 of the acyl chain. The large tunnel-shaped active site cavity observed in the mECI structure explains the relative substrate promiscuity in acyl-chain length and stereochemistry. Comparison with the crystal structure of pECI suggests the catalytic residues from both enzymes are spatially conserved but not in their primary structures, providing a powerful reminder of how catalytic residues cannot be determined solely by sequence alignments.
  Selected figure(s)  
Figure 1.
Figure 1. The overall fold of mECI and comparison with pECI. (A) Ribbon diagram of a single monomer, as found in the asymmetric unit. The color is ramped from blue, at the N terminus, to red, at the C terminus. Note the three -helices of the C-terminal self-association fold at the bottom and right of the figure. (B) Comparison of the trimeric assemblies of mECI (left), crotonase (middle), and MenB (right). The trimeric forms of the enzymes are viewed down the threefold crystallographic axis, with each subunit colored differently. All three models are in the same orientation, with the trimer-trimer interfaces of crotonase and MenB pointing up. The C-terminal domain is colored a darker shade than the N-terminal domain. Comparison of the three figures clearly shows variations in the C-terminal topology: the self-association fold in mECI, intra-trimer domain swapping fold in crotonase, and inter-trimer domain swapping fold in MenB. However, the arrangement of -helices within each monomer is similar. (C) Superimposition of the crystal structures of mECI, in purple, and pECI, colored light blue. Crotonyl-CoA molecules, as based on the octanoyl-CoA-crotonase complex, are included as darker colored sticks. (D) Comparison of the electrostatic surfaces of mECI (left) and pECI (right); contoured from + 10 kT/e, colored red, to +10 kT/e, colored blue. The models are in the same orientation, looking down the threefold axis, with the trimer-trimer interface of pECI facing up. The twofold axes that form the hexamer in pECI are perpendicular to the threefold axis. The distribution of negative charge between the two enzymes is very different.
Figure 5.
Figure 5. Proposed reaction mechanism for mECI, with Glu165 acting as both the general base and conjugate acid. Although the current mECI structure has no substrate analog bound, crotonyl-CoA has been modeled in. The carboxylate of Glu165 is about 3 from the C2 atom of the acyl chain of modeled substrate. The Glu165 to C4 atom distance is also ~3 for the cis conformation and ~4 in the trans conformation, implying that Glu165 might undergo minor conformational changes before reprotonating the C4 atom during catalysis. Backbone amide groups from Leu95 and Gly140 form hydrogen bonds to the thioester carbonyl oxygen, stabilizing the enolate intermediate.
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 1545-1555) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
17139085 P.M.Leonard, A.M.Brzozowski, A.Lebedev, C.M.Marshall, D.J.Smith, C.S.Verma, N.J.Walton, and G.Grogan (2006).
The 1.8 A resolution structure of hydroxycinnamoyl-coenzyme A hydratase-lyase (HCHL) from Pseudomonas fluorescens, an enzyme that catalyses the transformation of feruloyl-coenzyme A to vanillin.
  Acta Crystallogr D Biol Crystallogr, 62, 1494-1501.
PDB code: 2j5i
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