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PDBsum entry 1ofg

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1ofg
Jmol
Contents
Protein chains
(+ 0 more) 381 a.a. *
Ligands
NDP ×6
Waters ×840
* Residue conservation analysis
PDB id:
1ofg
Name: Oxidoreductase
Title: Glucose-fructose oxidoreductase
Structure: Glucose-fructose oxidoreductase. Chain: a, b, c, d, e, f. Ec: 1.1.99.28
Source: Zymomonas mobilis. Organism_taxid: 542. Cellular_location: periplasm
Biol. unit: Tetramer (from PDB file)
Resolution:
2.70Å     R-factor:   0.203    
Authors: R.L.Kingston,R.K.Scopes,E.N.Baker
Key ref:
R.L.Kingston et al. (1996). The structure of glucose-fructose oxidoreductase from Zymomonas mobilis: an osmoprotective periplasmic enzyme containing non-dissociable NADP. Structure, 4, 1413-1428. PubMed id: 8994968 DOI: 10.1016/S0969-2126(96)00149-9
Date:
17-Oct-96     Release date:   21-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q07982  (GFO_ZYMMO) -  Glucose--fructose oxidoreductase
Seq:
Struc:
433 a.a.
381 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.99.28  - Glucose-fructose oxidoreductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glucose + D-fructose = D-gluconolactone + D-glucitol
D-glucose
+ D-fructose
= D-gluconolactone
+ D-glucitol
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     oxidoreductase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(96)00149-9 Structure 4:1413-1428 (1996)
PubMed id: 8994968  
 
 
The structure of glucose-fructose oxidoreductase from Zymomonas mobilis: an osmoprotective periplasmic enzyme containing non-dissociable NADP.
R.L.Kingston, R.K.Scopes, E.N.Baker.
 
  ABSTRACT  
 
BACKGROUND: The organism Zymomonas mobilis occurs naturally in sugar-rich environments. To protect the bacterium against osmotic shock, the periplasmic enzyme glucose-fructose oxidoreductase (GFOR) produces the compatible, solute sorbitol by reduction of fructose, coupled with the oxidation of glucose to gluconolactone. Hence, Z mobilis can tolerate high concentrations of sugars and this property may be useful in the development of an efficient microbial process for ethanol production. Each enzyme subunit contains tightly associated NADP which is not released during the catalytic cycle. RESULTS: The structure of GFOR was determined by X-ray crystallography at 2.7 A resolution. Each subunit of the tetrameric enzyme comprises two domains, a classical dinucleotide-binding domain, and a C-terminal domain based on a predominantly antiparallel nine-stranded beta sheet. In the tetramer, the subunits associate to form two extended 18-stranded beta sheets, which pack against each other in a face to face fashion, creating an extensive interface at the core of the tetramer. An N-terminal arm from each subunit wraps around the dinucleotide-binding domain of an adjacent subunit, covering the adenine ring of NADP. CONCLUSIONS: In GFOR, the NADP is found associated with a classical dinucleotide-binding domain in a conventional fashion. The NADP is effectively buried in the protein-subunit interior as a result of interactions with the N-terminal arm from an adjacent subunit in the tetramer, and with a short helix from the C-terminal domain of the protein. This accounts for NADP's inability to dissociate. The N-terminal arm may also contribute to stabilization of the tetramer. The enzyme has an unexpected structural similarity with the cytoplasmic enzyme glucose-6-phosphate dehydrogenase (G6PD). We hypothesize that both enzymes have diverged from a common ancestor. The mechanism of catalysis is still unclear, but we have identified a conserved structural motif (Glu-Lys-Pro) in the active site of GFOR and G6PD that may be important for catalysis.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The active site of GFOR; atoms are shown in standard colors. Shows the interaction of the nicotinamide ring with Tyr42. (Figure generated using the program SETOR [78].)
 
  The above figure is reprinted by permission from Cell Press: Structure (1996, 4, 1413-1428) copyright 1996.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20809899 K.E.van Straaten, H.Zheng, D.R.Palmer, and D.A.Sanders (2010).
Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification.
  Biochem J, 432, 237-247.
PDB codes: 3mz0 3nt2 3nt4 3nt5 3nto 3ntq 3ntr
18701455 J.B.Thoden, L.A.Ryan, R.J.Reece, and H.M.Holden (2008).
The Interaction between an Acidic Transcriptional Activator and Its Inhibitor: THE MOLECULAR BASIS OF Gal4p RECOGNITION BY Gal80p.
  J Biol Chem, 283, 30266-30272.
PDB code: 3e1k
  18259059 K.E.Van Straaten, A.Hoffort, D.R.Palmer, and D.A.Sanders (2008).
Purification, crystallization and preliminary X-ray analysis of inositol dehydrogenase (IDH) from Bacillus subtilis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 98.  
18453689 V.Carbone, R.Sumii, S.Ishikura, Y.Asada, A.Hara, and O.El-Kabbani (2008).
Structure of monkey dimeric dihydrodiol dehydrogenase in complex with isoascorbic acid.
  Acta Crystallogr D Biol Crystallogr, 64, 532-542.
PDB code: 2poq
17654552 V.Carbone, S.Endo, R.Sumii, R.P.Chung, T.Matsunaga, A.Hara, and O.El-Kabbani (2008).
Structures of dimeric dihydrodiol dehydrogenase apoenzyme and inhibitor complex: probing the subunit interface with site-directed mutagenesis.
  Proteins, 70, 176-187.
PDB codes: 2o48 2o4u
17121853 J.B.Thoden, C.A.Sellick, R.J.Reece, and H.M.Holden (2007).
Understanding a transcriptional paradigm at the molecular level. The structure of yeast Gal80p.
  J Biol Chem, 282, 1534-1538.
PDB code: 2nvw
17216451 J.R.Wilkinson, J.Yu, J.M.Bland, W.C.Nierman, D.Bhatnagar, and T.E.Cleveland (2007).
Amino acid supplementation reveals differential regulation of aflatoxin biosynthesis in Aspergillus flavus NRRL 3357 and Aspergillus parasiticus SRRC 143.
  Appl Microbiol Biotechnol, 74, 1308-1319.  
17401360 Q.P.Liu, G.Sulzenbacher, H.Yuan, E.P.Bennett, G.Pietz, K.Saunders, J.Spence, E.Nudelman, S.B.Levery, T.White, J.M.Neveu, W.S.Lane, Y.Bourne, M.L.Olsson, B.Henrissat, and H.Clausen (2007).
Bacterial glycosidases for the production of universal red blood cells.
  Nat Biotechnol, 25, 454-464.
PDB codes: 2ixa 2ixb
16867978 A.Anders, H.Lilie, K.Franke, L.Kapp, J.Stelling, E.D.Gilles, and K.D.Breunig (2006).
The galactose switch in Kluyveromyces lactis depends on nuclear competition between Gal4 and Gal1 for Gal80 binding.
  J Biol Chem, 281, 29337-29348.  
16461673 A.Kühn, S.Yu, and F.Giffhorn (2006).
Catabolism of 1,5-anhydro-D-fructose in Sinorhizobium morelense S-30.7.5: discovery, characterization, and overexpression of a new 1,5-anhydro-D-fructose reductase and its application in sugar analysis and rare sugar synthesis.
  Appl Environ Microbiol, 72, 1248-1257.  
16632251 L.Bai, L.Li, H.Xu, K.Minagawa, Y.Yu, Y.Zhang, X.Zhou, H.G.Floss, T.Mahmud, and Z.Deng (2006).
Functional analysis of the validamycin biosynthetic gene cluster and engineered production of validoxylamine A.
  Chem Biol, 13, 387-397.  
15950477 C.A.Sellick, and R.J.Reece (2005).
Eukaryotic transcription factors as direct nutrient sensors.
  Trends Biochem Sci, 30, 405-412.  
15342590 U.Johnsen, and P.Schönheit (2004).
Novel xylose dehydrogenase in the halophilic archaeon Haloarcula marismortui.
  J Bacteriol, 186, 6198-6207.  
12057956 C.K.Raymond, E.H.Sims, A.Kas, D.H.Spencer, T.V.Kutyavin, R.G.Ivey, Y.Zhou, R.Kaul, J.B.Clendenning, and M.V.Olson (2002).
Genetic variation at the O-antigen biosynthetic locus in Pseudomonas aeruginosa.
  J Bacteriol, 184, 3614-3622.  
12351635 H.J.Hektor, H.Kloosterman, and L.Dijkhuizen (2002).
Identification of a magnesium-dependent NAD(P)(H)-binding domain in the nicotinoprotein methanol dehydrogenase from Bacillus methanolicus.
  J Biol Chem, 277, 46966-46973.  
11741911 K.Reuter, S.Sanderbrand, H.Jomaa, J.Wiesner, I.Steinbrecher, E.Beck, M.Hintz, G.Klebe, and M.T.Stubbs (2002).
Crystal structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase, a crucial enzyme in the non-mevalonate pathway of isoprenoid biosynthesis.
  J Biol Chem, 277, 5378-5384.
PDB code: 1k5h
11133954 N.Blaudeck, G.A.Sprenger, R.Freudl, and T.Wiegert (2001).
Specificity of signal peptide recognition in tat-dependent bacterial protein translocation.
  J Bacteriol, 183, 604-610.  
10652088 B.C.Berks, F.Sargent, and T.Palmer (2000).
The Tat protein export pathway.
  Mol Microbiol, 35, 260-274.  
11080625 E.Johansson, J.J.Steffens, Y.Lindqvist, and G.Schneider (2000).
Crystal structure of saccharopine reductase from Magnaporthe grisea, an enzyme of the alpha-aminoadipate pathway of lysine biosynthesis.
  Structure, 8, 1037-1047.
PDB codes: 1e5l 1e5q 1ff9
10745013 S.W.Au, S.Gover, V.M.Lam, and M.J.Adams (2000).
Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency.
  Structure, 8, 293-303.
PDB code: 1qki
10406965 D.Halbig, T.Wiegert, N.Blaudeck, R.Freudl, and G.A.Sprenger (1999).
The efficient export of NADP-containing glucose-fructose oxidoreductase to the periplasm of Zymomonas mobilis depends both on an intact twin-arginine motif in the signal peptide and on the generation of a structural export signal induced by cofactor binding.
  Eur J Biochem, 263, 543-551.  
10336376 R.Schleif (1999).
Arm-domain interactions in proteins: a review.
  Proteins, 34, 1-3.  
10087441 Y.S.Cheng, T.K.Tang, and M.Hwang (1999).
Amino acid conservation and clinical severity of human glucose-6-phosphate dehydrogenase mutations.
  J Biomed Sci, 6, 106-114.  
9501971 L.Aravind, and E.V.Koonin (1998).
Eukaryotic transcription regulators derive from ancient enzymatic domains.
  Curr Biol, 8, R111-R113.  
18576049 M.Silva-Martinez, D.Haltrich, S.Novalic, K.D.Kulbe, and B.Nidetzky (1998).
Simultaneous enzymatic synthesis of gluconic acid and sorbitol : Continuous process development using glucose-fructose oxidoreductase fromZymomonas mobilis.
  Appl Biochem Biotechnol, 70, 863-868.  
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.