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Oxidoreductase PDB id
1gyr
Jmol
Contents
Protein chains
364 a.a. *
Ligands
GOL ×11
SO4 ×9
Waters ×166
* Residue conservation analysis
PDB id:
1gyr
Name: Oxidoreductase
Title: Mutant form of enoyl thioester reductase from candida tropicalis
Structure: 2,4-dienoyl-coa reductase. Chain: a, b, c. Synonym: 2-enoyl thioester reductase. Engineered: yes. Mutation: yes
Source: Candida tropicalis. Yeast. Organism_taxid: 5482. Strain: pk233. Atcc: 20336. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Resolution:
2.60Å     R-factor:   0.195     R-free:   0.245
Authors: T.T.Airenne,J.M.Torkko,S.Van Der Plas,R.T.Sormunen, A.J.Kastaniotis,R.K.Wierenga,J.K.Hiltunen
Key ref:
T.T.Airenne et al. (2003). Structure-function analysis of enoyl thioester reductase involved in mitochondrial maintenance. J Mol Biol, 327, 47-59. PubMed id: 12614607 DOI: 10.1016/S0022-2836(03)00038-X
Date:
29-Apr-02     Release date:   13-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
Q8WZM3  (ETR1_CANTR) -  Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial
Seq:
Struc: 		386 a.a.
364 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: E.C.1.3.1.10  - Enoyl-[acyl-carrier-protein] reductase (Nadph, B-specific).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acyl-[acyl-carrier-protein] + NADP+ = trans-2,3-dehydroacyl-[acyl- carrier-protein] + NADPH
Acyl-[acyl-carrier-protein]
Bound ligand (Het Group name = GOL)
matches with 44.44% similarity 		+ NADP(+)
 = trans-2,3-dehydroacyl-[acyl- carrier-protein]
 + NADPH
   Enzyme class 2: E.C.1.3.1.38  - Trans-2-enoyl-CoA reductase (NADPH).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acyl-CoA + NADP+ = trans-2,3-dehydroacyl-CoA + NADPH
Acyl-CoA
 + NADP(+)
 = trans-2,3-dehydroacyl-CoA
 + NADPH
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(03)00038-X J Mol Biol 327:47-59 (2003)
PubMed id: 12614607  
 
 
Structure-function analysis of enoyl thioester reductase involved in mitochondrial maintenance.
T.T.Airenne, J.M.Torkko, S.Van den plas, R.T.Sormunen, A.J.Kastaniotis, R.K.Wierenga, J.K.Hiltunen.
 
  ABSTRACT  
 
Candida tropicalis enoyl thioester reductase Etr1p and the Saccharomyces cerevisiae homologue Mrf1p catalyse the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis (FAS). Unlike prokaryotic enoyl thioester reductases (ETRs), which belong to the short-chain dehydrogenases/reductases (SDR), Etr1p and Mrf1p represent structurally distinguishable ETRs that belong to the medium-chain dehydrogenases/reductases (MDR) superfamily, indicating independent origin of two separate classes of ETRs. The crystal structures of Etr1p, the Etr1p-NADPH complex and the Etr1Y79Np mutant were refined to 1.70A, 2.25A and 2.60A resolution, respectively. The native fold of Etr1p was maintained in Etr1Y79Np, but the mutant had only 0.1% of Etr1p catalytic activity remaining and failed to rescue the respiratory deficient phenotype of the mrf1Delta strain. Mutagenesis of Tyr73 in Mrf1p, corresponding to Tyr79 in Etr1p, produced similar results. Our data indicate that the mitochondrial reductase activity is indispensable for respiratory function in yeast, emphasizing the significance of Mrf1p (Etr1p) and mitochondrial FAS for the integrity of the respiratory competent organelle.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Conformational differences between NADPH bound and unbound forms of Etr1p. (A) Ribbon view of apo (grey) and holoenzyme (rainbow colouring) structures. The view in (B) is rotated -90° around the y-axis compared with the view in (A). (C) A zoom view of (B). The nicotinamide (Nic) and adenosine (Ade) moiety of NADPH as well as Y79 are labelled. The carbon atoms of the putative catalytic residue Y79 of the apo and holoenzyme are coloured grey and green, respectively. 		Figure 4.
Figure 4. NADPH binding. A stereo view showing the amino acid residues as well as structural water and glycerol molecules of the Etr1p-NADPH complex structure that have atoms less than 3.5 Å away from NADPH. Interactions between the ligand and the M299 residue (contact surface area >11 Å2), having the largest contact surface area (114 Å2) with NADPH, are shown with violet broken lines. The hydrogen bonds between amino acids and NADPH that have larger than 18 Å2 contact surface are also depicted (orange broken line). Water molecules are shown as blue spheres.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 47-59) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20835842 S.Porté, A.Moeini, I.Reche, N.Shafqat, U.Oppermann, J.Farrés, and X.Parés (2011).
Kinetic and structural evidence of the alkenal/one reductase specificity of human ΞΆ-crystallin.
  Cell Mol Life Sci, 68, 1065-1077.  
20662770 D.I.Chan, and H.J.Vogel (2010).
Current understanding of fatty acid biosynthesis and the acyl carrier protein.
  Biochem J, 430, 1.  
19151923 R.P.Massengo-Tiassé, and J.E.Cronan (2009).
Diversity in enoyl-acyl carrier protein reductases.
  Cell Mol Life Sci, 66, 1507-1517.  
19349281 S.Porté, E.Valencia, E.A.Yakovtseva, E.Borràs, N.Shafqat, J.E.Debreczeny, A.C.Pike, U.Oppermann, J.Farrés, I.Fita, and X.Parés (2009).
Three-dimensional Structure and Enzymatic Function of Proapoptotic Human p53-inducible Quinone Oxidoreductase PIG3.
  J Biol Chem, 284, 17194-17205.
PDB code: 2j8z
19458256 T.J.Erb, V.Brecht, G.Fuchs, M.Müller, and B.E.Alber (2009).
Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase.
  Proc Natl Acad Sci U S A, 106, 8871-8876.  
19286916 W.Q.Song, Y.M.Qin, M.Saito, T.Shirai, F.M.Pujol, A.J.Kastaniotis, J.K.Hiltunen, and Y.X.Zhu (2009).
Characterization of two cotton cDNAs encoding trans-2-enoyl-CoA reductase reveals a putative novel NADPH-binding motif.
  J Exp Bot, 60, 1839-1848.  
18772430 T.Maier, M.Leibundgut, and N.Ban (2008).
The crystal structure of a mammalian fatty acid synthase.
  Science, 321, 1315-1322.
PDB codes: 2vz8 2vz9
19000823 Y.H.Wu, T.P.Ko, R.T.Guo, S.M.Hu, L.M.Chuang, and A.H.Wang (2008).
Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2.
  Structure, 16, 1714-1723.
PDB codes: 2zb3 2zb4 2zb7 2zb8
16780361 S.Giri, J.R.Idle, C.Chen, T.M.Zabriskie, K.W.Krausz, and F.J.Gonzalez (2006).
A metabolomic approach to the metabolism of the areca nut alkaloids arecoline and arecaidine in the mouse.
  Chem Res Toxicol, 19, 818-827.  
15569691 M.Hoffmeister, M.Piotrowski, U.Nowitzki, and W.Martin (2005).
Mitochondrial trans-2-enoyl-CoA reductase of wax ester fermentation from Euglena gracilis defines a new family of enzymes involved in lipid synthesis.
  J Biol Chem, 280, 4329-4338.  
15549676 R.L.Rich, and D.G.Myszka (2005).
Survey of the year 2003 commercial optical biosensor literature.
  J Mol Recognit, 18, 1.  
15387819 A.J.Kastaniotis, K.J.Autio, R.T.Sormunen, and J.K.Hiltunen (2004).
Htd2p/Yhr067p is a yeast 3-hydroxyacyl-ACP dehydratase essential for mitochondrial function and morphology.
  Mol Microbiol, 53, 1407-1421.  
15229897 I.Levin, R.Schwarzenbacher, D.McMullan, P.Abdubek, E.Ambing, T.Biorac, J.Cambell, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, K.Quijano, R.Reyes, A.Robb, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, and I.A.Wilson (2004).
Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution.
  Proteins, 56, 629-633.
PDB code: 1vj1
15007077 T.Hori, T.Yokomizo, H.Ago, M.Sugahara, G.Ueno, M.Yamamoto, T.Kumasaka, T.Shimizu, and M.Miyano (2004).
Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop.
  J Biol Chem, 279, 22615-22623.
PDB codes: 1v3t 1v3u 1v3v
12654921 I.J.Miinalainen, Z.J.Chen, J.M.Torkko, P.L.Pirilä, R.T.Sormunen, U.Bergmann, Y.M.Qin, and J.K.Hiltunen (2003).
Characterization of 2-enoyl thioester reductase from mammals. An ortholog of YBR026p/MRF1'p of the yeast mitochondrial fatty acid synthesis type II.
  J Biol Chem, 278, 20154-20161.  
12890667 J.M.Torkko, K.T.Koivuranta, A.J.Kastaniotis, T.T.Airenne, T.Glumoff, M.Ilves, A.Hartig, A.Gurvitz, and J.K.Hiltunen (2003).
Candida tropicalis expresses two mitochondrial 2-enoyl thioester reductases that are able to form both homodimers and heterodimers.
  J Biol Chem, 278, 41213-41220.
PDB code: 1n9g
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 code is shown on the right.