PDBsum entry 1pjh

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Isomerase PDB id
Protein chains
259 a.a. *
SO4 ×10
GOL ×4
Waters ×382
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Structural studies on delta3-delta2-enoyl-coa isomerase: the mode of assembly of the trimeric disks of the crotonase sup
Structure: Enoyl-coa isomerase. Eci1p. Chain: a, b, c. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: eci1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PDB file)
2.10Å     R-factor:   0.168     R-free:   0.189
Authors: A.M.Mursula,J.K.Hiltunen,R.K.Wierenga
Key ref:
A.M.Mursula et al. (2004). Structural studies on delta(3)-delta(2)-enoyl-CoA isomerase: the variable mode of assembly of the trimeric disks of the crotonase superfamily. FEBS Lett, 557, 81-87. PubMed id: 14741345 DOI: 10.1016/S0014-5793(03)01450-9
03-Jun-03     Release date:   20-Jan-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q05871  (ECI1_YEAST) -  3,2-trans-enoyl-CoA isomerase
280 a.a.
259 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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     peroxisome   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  


    Added reference    
DOI no: 10.1016/S0014-5793(03)01450-9 FEBS Lett 557:81-87 (2004)
PubMed id: 14741345  
Structural studies on delta(3)-delta(2)-enoyl-CoA isomerase: the variable mode of assembly of the trimeric disks of the crotonase superfamily.
A.M.Mursula, J.K.Hiltunen, R.K.Wierenga.
Subunits of the enzymes in the crotonase superfamily form tight trimeric disks. In most members of this protein superfamily these disks assemble further into hexamers. Here we report on the 2.1 A structure of a tight hexameric crystal form of the yeast peroxisomal delta(3)-delta(2)-enoyl-CoA isomerase (Eci1p). A comparison of this structure to a previously solved crystal form of Eci1p and other structures of this superfamily shows that there is much variability with respect to the relative distance between the disks and their relative orientations. In particular helices H2 and H9 are involved in the inter-trimer contacts and there are considerable structural differences in these helices in this superfamily. Helices H2 and H9 are near the catalytic cavity and it is postulated that the observed structural variability of these helices, stabilized by the different modes of assembly, has allowed the evolution of the wide range of substrate and catalytic specificity within this enzyme superfamily.
  Selected figure(s)  
Figure 2.
Fig. 2. A: The superposition of the monomer fold of the tight hexamer form (yellow) and the loose hexamer form (green) of Eci1p. The helices facing the inter-trimer space, H1, H2, H9 and H8′, are labelled. The helix H8′ is from the neighboring subunit. Also shown are the catalytic residue Glu158 as well as Arg100, Asn101 (helix H2) and the oxyanion hole residues Ala70 and Leu126. The carbon atoms of Glu158, Arg100 and Asn101 of the loose hexamer structure are colored pink. N and C identify the amino-terminus and carboxy-terminus, respectively. B: The catalytic site of the tight hexamer form of Eci1p (as seen in subunit A). The side chain atoms of the catalytic glutamate Glu158 are hydrogen-bonded to Asn101, a glycerol molecule and wat19 of a buried cluster of four water molecules. Also shown are Arg100 (extending into the active site and hydrogen-bonded to Asn101) and oxyanion hole residues Ala70 and Leu126. Leu126 is at the beginning of helix H3. The figures were made with the program Pymol [25].
Figure 3.
Fig. 3. Comparison of the assembly of the Eci1p hexamers. A: The tight hexamer form of Eci1p. The subunit shown in the standard view (as in Fig. 2) is labelled at the N-terminus; also labelled are helices H1, H2, H9 and H8′ which provide most of the inter-trimer contacts. B: The loose hexamer form of Eci1p [12]. The figures were made with the program Pymol [25]. Corresponding subunits in A and B are colored with the same colors, such as to visualize the relative rotation of the upper trimer with respect to the (stationary) lower trimer.
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2004, 557, 81-87) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18831052 K.Kurimoto, K.Kuwasako, A.M.Sandercock, S.Unzai, C.V.Robinson, Y.Muto, and S.Yokoyama (2009).
AU-rich RNA-binding induces changes in the quaternary structure of AUH.
  Proteins, 75, 360-372.
PDB codes: 2zqq 2zqr
16096274 M.C.Sleeman, J.L.Sorensen, E.T.Batchelar, M.A.McDonough, and C.J.Schofield (2005).
Structural and mechanistic studies on carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily catalyzing the first step in carbapenem biosynthesis.
  J Biol Chem, 280, 34956-34965.
PDB codes: 2a7k 2a81
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
15583385 P.M.Leonard, C.M.Marshall, E.J.Dodson, N.J.Walton, and G.Grogan (2004).
Purification, crystallization and preliminary X-ray crystallographic analysis of hydroxycinnamoyl-coenzyme A hydratase-lyase (HCHL), a crotonase homologue active in phenylpropanoid metabolism.
  Acta Crystallogr D Biol Crystallogr, 60, 2343-2345.  
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.