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PDBsum entry 1hnu

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Isomerase PDB id
1hnu
Jmol
Contents
Protein chain
248 a.a. *
Ligands
REO ×2
EDO ×2
Waters ×194
* Residue conservation analysis
PDB id:
1hnu
Name: Isomerase
Title: Crystal structure of peroxisomal delta3-delta2-enoyl-coa iso from saccharomyces cerevisiae
Structure: D3,d2-enoyl coa isomerase eci1. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
Resolution:
2.15Å     R-factor:   0.215     R-free:   0.257
Authors: A.M.Mursula,D.M.F.Van Aalten,J.K.Hiltunen,R.K.Wierenga
Key ref:
A.M.Mursula et al. (2001). The crystal structure of delta(3)-delta(2)-enoyl-CoA isomerase. J Mol Biol, 309, 845-853. PubMed id: 11399063 DOI: 10.1006/jmbi.2001.4671
Date:
08-Dec-00     Release date:   20-Jun-01    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q05871  (ECI1_YEAST) -  3,2-trans-enoyl-CoA isomerase
Seq:
Struc:
280 a.a.
248 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.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
= (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: 10.1006/jmbi.2001.4671 J Mol Biol 309:845-853 (2001)
PubMed id: 11399063  
 
 
The crystal structure of delta(3)-delta(2)-enoyl-CoA isomerase.
A.M.Mursula, D.M.van Aalten, J.K.Hiltunen, R.K.Wierenga.
 
  ABSTRACT  
 
The active-site geometry of the first crystal structure of a Delta(3)-Delta(2)-enoyl-coenzyme A (CoA) isomerase (the peroxisomal enzyme from the yeast Saccharomyces cerevisiae) shows that only one catalytic base, Glu158, is involved in shuttling the proton from the C2 carbon atom of the substrate, Delta(3)-enoyl-CoA, to the C4 atom of the product, Delta(2)-enoyl-CoA. Site-directed mutagenesis has been performed to confirm that this glutamate residue is essential for catalysis. This Delta(3)-Delta(2)-enoyl-CoA isomerase is a hexameric enzyme, consisting of six identical subunits. It belongs to the hydratase/isomerase superfamily of enzymes which catalyze a wide range of CoA-dependent reactions. The members of the hydratase/ isomerase superfamily have only a low level of sequence identity. Comparison of the crystal structure of the Delta(3)-Delta(2)-enoyl-CoA isomerase with the other structures of this superfamily shows only one region of large structural variability, which is in the second turn of the spiral fold and which is involved in defining the shape of the binding pocket.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The reaction mechanism catalyzed by enoyl-CoA isomerase. The fatty acid tail can be of variable length. The two NH groups are peptide NH groups making an oxyanion hole. The reaction intermediate (shown in brackets) is stabilized by hydrogen-bonding interactions of the thioester oxygen atom in the oxyanion hole (see the text). From the structure of enoyl-CoA isomerase it can be deduced that there is only one base (B) which is Glu158. The enoyl-CoA isomerase studied here is from yeast (S. cerevisiae) peroxisomes. The enzyme, expressed in E. coli, was encoded by the full-length isomerase gene (ECI1)[8]. The isomerase-activity assays were performed according to published methods [26] using 60 µM trans-3-hexenoyl-CoA as substrate. The mutagenesis of Glu158 to alanine was done using the QuickChange(TM) mutagenesis kit (Stratagene) following the manufacturer's instructions. The expression and purification of the E158A variant were performed as for the wild-type.[8 and 25] Gel-filtration studies showed similar elution patterns for the E158A variant and the wild-type, in good agreement with the hexamer. [8]
Figure 3.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 309, 845-853) copyright 2001.  
  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
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
18655062 A.Liavonchanka, and I.Feussner (2008).
Biochemistry of PUFA double bond isomerases producing conjugated linoleic acid.
  Chembiochem, 9, 1867-1872.  
18725356 B.K.Zolman, N.Martinez, A.Millius, A.R.Adham, and B.Bartel (2008).
Identification and characterization of Arabidopsis indole-3-butyric acid response mutants defective in novel peroxisomal enzymes.
  Genetics, 180, 237-251.  
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
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
16131752 J.M.Johnston, V.L.Arcus, and E.N.Baker (2005).
Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms.
  Acta Crystallogr D Biol Crystallogr, 61, 1199-1206.  
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.  
15138275 P.M.Leonard, and G.Grogan (2004).
Structure of 6-oxo camphor hydrolase H122A mutant bound to its natural product, (2S,4S)-alpha-campholinic acid: mutant structure suggests an atypical mode of transition state binding for a crotonase homolog.
  J Biol Chem, 279, 31312-31317.
PDB code: 1szo
12663926 H.Zhang, Z.Yang, Y.Shen, and L.Tong (2003).
Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase.
  Science, 299, 2064-2067.
PDB codes: 1od2 1od4
12909628 J.J.Truglio, K.Theis, Y.Feng, R.Gajda, C.Machutta, P.J.Tonge, and C.Kisker (2003).
Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis.
  J Biol Chem, 278, 42352-42360.
PDB codes: 1q51 1q52
12697341 J.K.Hiltunen, A.M.Mursula, H.Rottensteiner, R.K.Wierenga, A.J.Kastaniotis, and A.Gurvitz (2003).
The biochemistry of peroxisomal beta-oxidation in the yeast Saccharomyces cerevisiae.
  FEMS Microbiol Rev, 27, 35-64.  
11781327 D.Zhang, W.Yu, B.V.Geisbrecht, S.J.Gould, H.Sprecher, and H.Schulz (2002).
Functional characterization of Delta3,Delta2-enoyl-CoA isomerases from rat liver.
  J Biol Chem, 277, 9127-9132.  
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.