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PDBsum entry 1eno

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Oxidoreductase PDB id
1eno
Jmol
Contents
Protein chain
297 a.a. *
Ligands
NAD
Waters ×110
* Residue conservation analysis
PDB id:
1eno
Name: Oxidoreductase
Title: Brassica napus enoyl acp reductase/NAD binary complex at ph room temperature
Structure: Enoyl acyl carrier protein reductase. Chain: a. Engineered: yes. Mutation: yes
Source: Brassica napus. Rape. Organism_taxid: 3708. Organ: seed. Tissue: seed. Gene: pear7 clone. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
1.90Å     R-factor:   0.164    
Authors: J.B.Rafferty,D.W.Rice
Key ref:
J.B.Rafferty et al. (1995). Common themes in redox chemistry emerge from the X-ray structure of oilseed rape (Brassica napus) enoyl acyl carrier protein reductase. Structure, 3, 927-938. PubMed id: 8535786 DOI: 10.1016/S0969-2126(01)00227-1
Date:
18-Oct-95     Release date:   14-Oct-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80030  (FABI_BRANA) -  Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic
Seq:
Struc:
385 a.a.
297 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.3.1.9  - Enoyl-[acyl-carrier-protein] reductase (NADH).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An acyl-[acyl-carrier protein] + NAD+ = a trans-2,3-dehydroacyl-[acyl- carrier protein] + NADH
acyl-[acyl-carrier protein]
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
= trans-2,3-dehydroacyl-[acyl- carrier protein]
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     enoyl-[acyl-carrier-protein] reductase (NADH) activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(01)00227-1 Structure 3:927-938 (1995)
PubMed id: 8535786  
 
 
Common themes in redox chemistry emerge from the X-ray structure of oilseed rape (Brassica napus) enoyl acyl carrier protein reductase.
J.B.Rafferty, J.W.Simon, C.Baldock, P.J.Artymiuk, P.J.Baker, A.R.Stuitje, A.R.Slabas, D.W.Rice.
 
  ABSTRACT  
 
BACKGROUND: Enoyl acyl carrier protein reductase (ENR) catalyzes the NAD(P)H-dependent reduction of trans-delta 2-enoyl acyl carrier protein, an essential step in de novo fatty acid biosynthesis. Plants contain both NADH-dependent and separate NADPH-dependent ENR enzymes which form part of the dissociable type II fatty acid synthetase. Highly elevated levels of the NADH-dependent enzyme are found during lipid deposition in maturing seeds of oilseed rape (Brassica napus). RESULTS: The crystal structure of an ENR-NAD binary complex has been determined at 1.9 A resolution and consists of a homotetramer in which each subunit forms a single domain comprising a seven-stranded parallel beta sheet flanked by seven alpha helices. The subunit has a topology highly reminiscent of a dinucleotide-binding fold. The active site has been located by difference Fourier analysis of data from crystals equilibrated in NADH. CONCLUSIONS: The structure of ENR shows a striking similarity with the epimerases and short-chain alcohol dehydrogenases, in particular, 3 alpha,20 beta-hydroxysteroid dehydrogenase (HSD). The similarity with HSD extends to the conservation of a catalytically important lysine that stabilizes the transition state and to the use of a tyrosine as a base--with subtle modifications arising from differing requirements of the reduction chemistry.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Stereo diagram of the ENR tetramer viewed along one of three molecular twofold axes (the R axis; see text). Subunits are numbered 1 (light blue), 2 (yellow), 3 (dark blue) and 4 (green) with α helices and β strands shown as coiled ribbons and flattened arrows, respectively. The NADH cofactor is shown in all-atom representation and coloured by atom type. (Produced using the program MIDAS [51].). Figure 4. Stereo diagram of the ENR tetramer viewed along one of three molecular twofold axes (the R axis; see text). Subunits are numbered 1 (light blue), 2 (yellow), 3 (dark blue) and 4 (green) with α helices and β strands shown as coiled ribbons and flattened arrows, respectively. The NADH cofactor is shown in all-atom representation and coloured by atom type. (Produced using the program MIDAS [[3]51].).
Figure 12.
Figure 12. Stereoview of the superimposition of ENR and HSD near the nicotinamide ring of the NADH cofactor. The Cα backbone traces are shown in orange for ENR and cyan for HSD with key tyrosine and lysine residues (see text) shown in orange (ENR) and green (HSD). The NADH cofactors are shown in ball-and-stick representation in red for ENR and yellow for HSD. (Produced using the program MIDAS [51].). Figure 12. Stereoview of the superimposition of ENR and HSD near the nicotinamide ring of the NADH cofactor. The Cα backbone traces are shown in orange for ENR and cyan for HSD with key tyrosine and lysine residues (see text) shown in orange (ENR) and green (HSD). The NADH cofactors are shown in ball-and-stick representation in red for ENR and yellow for HSD. (Produced using the program MIDAS [[3]51].).
 
  The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 927-938) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20055482 H.Lu, and P.J.Tonge (2010).
Mechanism and inhibition of the FabV enoyl-ACP reductase from Burkholderia mallei.
  Biochemistry, 49, 1281-1289.  
19550039 M.J.Li, A.Q.Li, H.Xia, C.Z.Zhao, C.S.Li, S.B.Wan, Y.P.Bi, and X.J.Wang (2009).
Cloning and sequence analysis of putative type II fatty acid synthase genes from Arachis hypogaea L.
  J Biosci, 34, 227-238.  
19151923 R.P.Massengo-Tiassé, and J.E.Cronan (2009).
Diversity in enoyl-acyl carrier protein reductases.
  Cell Mol Life Sci, 66, 1507-1517.  
19011750 K.L.Kavanagh, H.Jörnvall, B.Persson, and U.Oppermann (2008).
Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes.
  Cell Mol Life Sci, 65, 3895-3906.  
17112527 D.J.Ferguson, S.A.Campbell, F.L.Henriquez, L.Phan, E.Mui, T.A.Richards, S.P.Muench, M.Allary, J.Z.Lu, S.T.Prigge, F.Tomley, M.W.Shirley, D.W.Rice, R.McLeod, and C.W.Roberts (2007).
Enzymes of type II fatty acid synthesis and apicoplast differentiation and division in Eimeria tenella.
  Int J Parasitol, 37, 33-51.  
  17697396 J.Z.Lu, S.P.Muench, M.Allary, S.Campbell, C.W.Roberts, E.Mui, R.L.McLeod, D.W.Rice, and S.T.Prigge (2007).
Type I and type II fatty acid biosynthesis in Eimeria tenella: enoyl reductase activity and structure.
  Parasitology, 134, 1949-1962.
PDB code: 2ptg
  17329825 K.H.Kim, J.K.Park, B.H.Ha, J.H.Moon, and E.E.Kim (2007).
Crystallization and preliminary X-ray crystallographic analysis of enoyl-ACP reductase III (FabL) from Bacillus subtilis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 246-248.  
15952903 S.W.White, J.Zheng, Y.M.Zhang, and Rock (2005).
The structural biology of type II fatty acid biosynthesis.
  Annu Rev Biochem, 74, 791-831.  
15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
  Proteins, 56, 130-142.  
15756459 P.W.Howe (2004).
A straight-forward method of optimising protein solubility for NMR.
  J Biomol NMR, 30, 283-286.  
14693546 S.Ducasse-Cabanot, M.Cohen-Gonsaud, H.Marrakchi, M.Nguyen, D.Zerbib, J.Bernadou, M.Daffé, G.Labesse, and A.Quémard (2004).
In vitro inhibition of the Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein reductase MabA by isoniazid.
  Antimicrob Agents Chemother, 48, 242-249.  
15133034 Y.M.Zhang, and C.O.Rock (2004).
Evaluation of epigallocatechin gallate and related plant polyphenols as inhibitors of the FabG and FabI reductases of bacterial type II fatty-acid synthase.
  J Biol Chem, 279, 30994-31001.  
14635124 A.Berchanski, and M.Eisenstein (2003).
Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry.
  Proteins, 53, 817-829.  
12832774 S.P.Muench, J.B.Rafferty, R.McLeod, D.W.Rice, and S.T.Prigge (2003).
Expression, purification and crystallization of the Plasmodium falciparum enoyl reductase.
  Acta Crystallogr D Biol Crystallogr, 59, 1246-1248.  
14635134 W.L.Duax, V.Pletnev, A.Addlagatta, J.Bruenn, and C.M.Weeks (2003).
Rational proteomics I. Fingerprint identification and cofactor specificity in the short-chain oxidoreductase (SCOR) enzyme family.
  Proteins, 53, 931-943.  
12192068 C.A.Bottoms, P.E.Smith, and J.J.Tanner (2002).
A structurally conserved water molecule in Rossmann dinucleotide-binding domains.
  Protein Sci, 11, 2125-2137.  
12037321 H.H.Lee, J.Yun, J.Moon, B.W.Han, B.I.Lee, J.Y.Lee, and S.W.Suh (2002).
Crystallization and preliminary X-ray crystallographic analysis of enoyl-acyl carrier protein reductase from Helicobacter pylori.
  Acta Crystallogr D Biol Crystallogr, 58, 1071-1073.  
11792710 R.Perozzo, M.Kuo, A.S.Sidhu, J.T.Valiyaveettil, R.Bittman, W.R.Jacobs, D.A.Fidock, and J.C.Sacchettini (2002).
Structural elucidation of the specificity of the antibacterial agent triclosan for malarial enoyl acyl carrier protein reductase.
  J Biol Chem, 277, 13106-13114.
PDB codes: 1nhd 1nhg 1nhw 1nnu 1vrw
11306095 T.Lanisnik Rizner, J.Stojan, and J.Adamski (2001).
17beta-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus: structural and functional aspects.
  Chem Biol Interact, 130, 793-803.  
10828945 A.Schmidt, H.Wu, R.E.MacKenzie, V.J.Chen, J.R.Bewly, J.E.Ray, J.E.Toth, and M.Cygler (2000).
Structures of three inhibitor complexes provide insight into the reaction mechanism of the human methylenetetrahydrofolate dehydrogenase/cyclohydrolase.
  Biochemistry, 39, 6325-6335.
PDB codes: 1dia 1dib 1dig
10848978 J.Benach, S.Atrian, J.Fibla, R.Gonzàlez-Duarte, and R.Ladenstein (2000).
Structure-function relationships in Drosophila melanogaster alcohol dehydrogenase allozymes ADH(S), ADH(F) and ADH(UF), and distantly related forms.
  Eur J Biochem, 267, 3613-3622.  
10801480 M.Fisher, J.T.Kroon, W.Martindale, A.R.Stuitje, A.R.Slabas, and J.B.Rafferty (2000).
The X-ray structure of Brassica napus beta-keto acyl carrier protein reductase and its implications for substrate binding and catalysis.
  Structure, 8, 339-347.
PDB code: 1edo
10666637 M.Fisher, S.E.Sedelnikova, W.Martindale, N.C.Thomas, J.W.Simon, A.R.Slabas, and J.B.Rafferty (2000).
Crystallization of the NADP-dependent beta-keto acyl-carrier protein reductase from Brassica napus.
  Acta Crystallogr D Biol Crystallogr, 56, 86-88.  
10521472 A.Roujeinikova, S.Sedelnikova, G.J.de Boer, A.R.Stuitje, A.R.Slabas, J.B.Rafferty, and D.W.Rice (1999).
Inhibitor binding studies on enoyl reductase reveal conformational changes related to substrate recognition.
  J Biol Chem, 274, 30811-30817.
PDB code: 1cwu
10387002 A.Yamashita, H.Kato, S.Wakatsuki, T.Tomizaki, T.Nakatsu, K.Nakajima, T.Hashimoto, Y.Yamada, and J.Oda (1999).
Structure of tropinone reductase-II complexed with NADP+ and pseudotropine at 1.9 A resolution: implication for stereospecific substrate binding and catalysis.
  Biochemistry, 38, 7630-7637.
PDB code: 2ae2
10336454 D.A.Rozwarski, C.Vilchèze, M.Sugantino, R.Bittman, and J.C.Sacchettini (1999).
Crystal structure of the Mycobacterium tuberculosis enoyl-ACP reductase, InhA, in complex with NAD+ and a C16 fatty acyl substrate.
  J Biol Chem, 274, 15582-15589.
PDB code: 1bvr
10027962 G.J.de Boer, G.J.Pielage, H.J.Nijkamp, A.R.Slabas, J.B.Rafferty, C.Baldock, D.W.Rice, and A.R.Stuitje (1999).
Molecular genetic analysis of enoyl-acyl carrier protein reductase inhibition by diazaborine.
  Mol Microbiol, 31, 443-450.  
10547700 L.J.Shimkets (1999).
Intercellular signaling during fruiting-body development of Myxococcus xanthus.
  Annu Rev Microbiol, 53, 525-549.  
10473585 M.J.van der Werf, C.van der Ven, F.Barbirato, M.H.Eppink, J.A.de Bont, and W.J.van Berkel (1999).
Stereoselective carveol dehydrogenase from Rhodococcus erythropolis DCL14. A novel nicotinoprotein belonging to the short chain dehydrogenase/reductase superfamily.
  J Biol Chem, 274, 26296-26304.  
10793890 R.J.Weselake, and D.C.Taylor (1999).
The study of storage lipid biosynthesis using microspore-derived cultures of oil seed rape.
  Prog Lipid Res, 38, 401-460.  
10480878 S.Menon, M.Stahl, R.Kumar, G.Y.Xu, and F.Sullivan (1999).
Stereochemical course and steady state mechanism of the reaction catalyzed by the GDP-fucose synthetase from Escherichia coli.
  J Biol Chem, 274, 26743-26750.  
  10595560 X.Qiu, C.A.Janson, R.I.Court, M.G.Smyth, D.J.Payne, and S.S.Abdel-Meguid (1999).
Molecular basis for triclosan activity involves a flipping loop in the active site.
  Protein Sci, 8, 2529-2532.
PDB code: 1c14
9652124 B.J.Rawlings (1998).
Biosynthesis of fatty acids and related metabolites.
  Nat Prod Rep, 15, 275-308.  
9761917 J.B.Rafferty, M.Fisher, S.J.Langridge, W.Martindale, N.C.Thomas, J.W.Simon, S.Bithell, A.R.Slabas, and D.W.Rice (1998).
Crystallization of the NADP-dependent beta-keto acyl carrier protein reductase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 54, 427-429.  
9521731 J.Luba, B.Nare, P.H.Liang, K.S.Anderson, S.M.Beverley, and L.W.Hardy (1998).
Leishmania major pteridine reductase 1 belongs to the short chain dehydrogenase family: stereochemical and kinetic evidence.
  Biochemistry, 37, 4093-4104.  
9765262 J.Thompson, A.Pikis, S.B.Ruvinov, B.Henrissat, H.Yamamoto, and J.Sekiguchi (1998).
The gene glvA of Bacillus subtilis 168 encodes a metal-requiring, NAD(H)-dependent 6-phospho-alpha-glucosidase. Assignment to family 4 of the glycosylhydrolase superfamily.
  J Biol Chem, 273, 27347-27356.  
9862812 W.S.Somers, M.L.Stahl, and F.X.Sullivan (1998).
GDP-fucose synthetase from Escherichia coli: structure of a unique member of the short-chain dehydrogenase/reductase family that catalyzes two distinct reactions at the same active site.
  Structure, 6, 1601-1612.
PDB codes: 1bsv 1fxs 1gfs
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9270971 A.Ziegler, S.M.Macintosh, L.Torrance, W.Simon, and A.R.Slabas (1997).
Recombinant antibody fragments that detect enoyl acyl carrier protein reductase in Brassica napus.
  Lipids, 32, 805-809.  
8939741 A.Andersson, D.Jordan, G.Schneider, and Y.Lindqvist (1996).
Crystal structure of the ternary complex of 1,3,8-trihydroxynaphthalene reductase from Magnaporthe grisea with NADPH and an active-site inhibitor.
  Structure, 4, 1161-1170.
PDB code: 1ybv
9022698 H.Bergler, S.Fuchsbichler, G.Högenauer, and F.Turnowsky (1996).
The enoyl-[acyl-carrier-protein] reductase (FabI) of Escherichia coli, which catalyzes a key regulatory step in fatty acid biosynthesis, accepts NADH and NADPH as cofactors and is inhibited by palmitoyl-CoA.
  Eur J Biochem, 242, 689-694.  
8805534 M.Leesong, B.S.Henderson, J.R.Gillig, J.M.Schwab, and J.L.Smith (1996).
Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site.
  Structure, 4, 253-264.
PDB codes: 1mka 1mkb
8564538 P.J.Artymiuk, A.R.Poirrette, D.W.Rice, and P.Willett (1996).
Biotin carboxylase comes into the fold.
  Nat Struct Biol, 3, 128-132.  
8994882 W.L.Duax, J.F.Griffin, and D.Ghosh (1996).
The fascinating complexities of steroid-binding enzymes.
  Curr Opin Struct Biol, 6, 813-823.  
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.