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PDBsum entry 1gox

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Oxidoreductase (oxygen(a)) PDB id
1gox
Jmol
Contents
Protein chain
351 a.a. *
Ligands
FMN
Waters ×298
* Residue conservation analysis
PDB id:
1gox
Name: Oxidoreductase (oxygen(a))
Title: Refined structure of spinach glycolate oxidase at 2 angstrom resolution
Structure: (S)-2-hydroxy-acid oxidase, peroxisomal. Chain: a. Engineered: yes
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.189    
Authors: Y.Lindqvist
Key ref: Y.Lindqvist (1989). Refined structure of spinach glycolate oxidase at 2 A resolution. J Mol Biol, 209, 151-166. PubMed id: 2681790
Date:
14-Jun-89     Release date:   15-Oct-89    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05414  (GOX_SPIOL) -  Peroxisomal (S)-2-hydroxy-acid oxidase
Seq:
Struc:
369 a.a.
350 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.3.15  - (S)-2-hydroxy-acid oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-2-hydroxy acid + O2 = 2-oxo acid + H2O2
(S)-2-hydroxy acid
+ O(2)
= 2-oxo acid
+ H(2)O(2)
      Cofactor: FMN
FMN
Bound ligand (Het Group name = FMN) corresponds exactly
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     oxidation-reduction process   3 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
J Mol Biol 209:151-166 (1989)
PubMed id: 2681790  
 
 
Refined structure of spinach glycolate oxidase at 2 A resolution.
Y.Lindqvist.
 
  ABSTRACT  
 
The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was obtained for 32,888 independent reflections from 5.5 to 2 A resolution. The geometry of the model, consisting of 350 amino acid residues, the cofactor flavin mononucleotide and 298 solvent molecules, is close to ideal with root-mean-square deviations of 0.015 A in bond lengths and 2.6 degrees in bond angles. The expected trimodal distribution with preference for staggered conformation is obtained for the side-chain chi 1-angles. The core of the subunit is built up from the eight beta-strands in the beta/alpha-barrel. This core consists of two hydrophobic layers. One in the center is made up of residues pointing in from the beta-strands towards the barrel axis and the second, consisting of two segments of residues, pointing out from the beta-strands towards the eight alpha-helices of the barrel and pointing from the helices towards the strands. The hydrogen bond pattern for the beta-strands in the beta/alpha-barrel is described. There are a number of residues with 3(10)-helix conformation, in particular there is one left-handed helix. The ordered solvent molecules are organized mainly in clusters. The average isotropic temperature factor is quite high, 27.1 A2, perhaps a reflection of the high solvent content in the crystal. The octameric glycolate oxidase molecule, which has 422 symmetry, makes strong interactions around the 4-fold axis forming a tight tetramer, but only weak interactions between the two tetramers forming the octamer.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20014430 S.Das, J.H.Glenn, and M.Subramanian (2010).
Enantioselective oxidation of 2-hydroxy carboxylic acids by glycolate oxidase and catalase coexpressed in methylotrophic Pichia pastoris.
  Biotechnol Prog, 26, 607-615.  
19758989 A.Pennati, and G.Gadda (2009).
Involvement of ionizable groups in catalysis of human liver glycolate oxidase.
  J Biol Chem, 284, 31214-31222.  
19465768 N.Sukumar, A.Dewanti, A.Merli, G.L.Rossi, B.Mitra, and F.S.Mathews (2009).
Structures of the G81A mutant form of the active chimera of (S)-mandelate dehydrogenase and its complex with two of its substrates.
  Acta Crystallogr D Biol Crystallogr, 65, 543-552.
PDB codes: 2a7n 2a7p 2a85 3giy
18215067 M.S.Murray, R.P.Holmes, and W.T.Lowther (2008).
Active site and loop 4 movements within human glycolate oxidase: implications for substrate specificity and drug design.
  Biochemistry, 47, 2439-2449.
PDB codes: 2rdt 2rdu 2rdw
  17142893 I.Leiros, E.Wang, T.Rasmussen, E.Oksanen, H.Repo, S.B.Petersen, P.Heikinheimo, and E.Hough (2006).
The 2.1 A structure of Aerococcus viridans L-lactate oxidase (LOX).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1185-1190.
PDB code: 2j6x
16314970 H.Kaneko, H.Minagawa, and J.Shimada (2005).
Rational design of thermostable lactate oxidase by analyzing quaternary structure and prevention of deamidation.
  Biotechnol Lett, 27, 1777-1784.  
  16511063 Y.Umena, K.Yorita, T.Matsuoka, M.Abe, A.Kita, K.Fukui, T.Tsukihara, and Y.Morimoto (2005).
Crystallization and preliminary X-ray diffraction study of L-lactate oxidase (LOX), R181M mutant, from Aerococcus viridans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 439-441.  
15226299 J.Singh, G.A.Khan, L.Kinarsky, H.Cheng, J.Wilken, K.H.Choi, E.Bedows, S.Sherman, and P.W.Cheng (2004).
Identification of disulfide bonds among the nine core 2 N-acetylglucosaminyltransferase-M cysteines conserved in the mucin beta6-N-acetylglucosaminyltransferase family.
  J Biol Chem, 279, 38969-38977.  
14604988 N.Sukumar, A.R.Dewanti, B.Mitra, and F.S.Mathews (2004).
High resolution structures of an oxidized and reduced flavoprotein. The water switch in a soluble form of (S)-mandelate dehydrogenase.
  J Biol Chem, 279, 3749-3757.
PDB codes: 1p4c 1p5b
15016352 S.W.Aufhammer, E.Warkentin, H.Berk, S.Shima, R.K.Thauer, and U.Ermler (2004).
Coenzyme binding in F420-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family.
  Structure, 12, 361-370.
PDB code: 1rhc
14596603 A.R.Dewanti, and B.Mitra (2003).
A transient intermediate in the reaction catalyzed by (S)-mandelate dehydrogenase from Pseudomonas putida.
  Biochemistry, 42, 12893-12901.  
12919327 H.Minagawa, J.Shimada, and H.Kaneko (2003).
Effect of mutations at Glu160 and Val198 on the thermostability of lactate oxidase.
  Eur J Biochem, 270, 3628-3633.  
11377202 C.Breithaupt, J.Strassner, U.Breitinger, R.Huber, P.Macheroux, A.Schaller, and T.Clausen (2001).
X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE.
  Structure, 9, 419-429.
PDB codes: 1icp 1icq 1ics
11559361 M.Gondry, J.Dubois, M.Terrier, and F.Lederer (2001).
The catalytic role of tyrosine 254 in flavocytochrome b2 (L-lactate dehydrogenase from baker's yeast). Comparison between the Y254F and Y254L mutant proteins.
  Eur J Biochem, 268, 4918-4927.  
11248020 S.Crosson, and K.Moffat (2001).
Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction.
  Proc Natl Acad Sci U S A, 98, 2995-3000.
PDB code: 1g28
10986463 A.Albert, M.Martínez-Ripoll, A.Espinosa-Ruiz, L.Yenush, F.A.Culiáñez-Macià, and R.Serrano (2000).
The X-ray structure of the FMN-binding protein AtHal3 provides the structural basis for the activity of a regulatory subunit involved in signal transduction.
  Structure, 8, 961-969.
PDB code: 1e20
10955993 I.E.Lehoux, and B.Mitra (2000).
Role of arginine 277 in (S)-mandelate dehydrogenase from Pseudomonas putida in substrate binding and transition state stabilization.
  Biochemistry, 39, 10055-10065.  
10944103 P.D.Pawelek, J.Cheah, R.Coulombe, P.Macheroux, S.Ghisla, and A.Vrielink (2000).
The structure of L-amino acid oxidase reveals the substrate trajectory into an enantiomerically conserved active site.
  EMBO J, 19, 4204-4215.
PDB codes: 1f8r 1f8s
10712739 Z.Fan, G.B.Oguntimein, and P.J.Reilly (2000).
Characterization of kinetics and thermostability of Acremonium strictum glucooligosaccharide oxidase.
  Biotechnol Bioeng, 68, 231-237.  
9271497 F.G.Whitby, H.Luecke, P.Kuhn, J.R.Somoza, J.A.Huete-Perez, J.D.Phillips, C.P.Hill, R.J.Fletterick, and C.C.Wang (1997).
Crystal structure of Tritrichomonas foetus inosine-5'-monophosphate dehydrogenase and the enzyme-product complex.
  Biochemistry, 36, 10666-10674.
PDB code: 1ak5
9020763 J.J.Tanner, M.D.Miller, K.S.Wilson, S.C.Tu, and K.L.Krause (1997).
Structure of bacterial luciferase beta 2 homodimer: implications for flavin binding.
  Biochemistry, 36, 665-672.
PDB code: 1xkj
  9144771 K.Stenberg, and Y.Lindqvist (1997).
Three-dimensional structures of glycolate oxidase with bound active-site inhibitors.
  Protein Sci, 6, 1009-1015.
PDB codes: 1al7 1al8
9220981 M.Tegoni, M.Gervais, and A.Desbois (1997).
Resonance Raman study on the oxidized and anionic semiquinone forms of flavocytochrome b2 and L-lactate monooxygenase. Influence of the structure and environment of the isoalloxazine ring on the flavin function.
  Biochemistry, 36, 8932-8946.  
9032071 P.Rowland, F.S.Nielsen, K.F.Jensen, and S.Larsen (1997).
The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis.
  Structure, 5, 239-252.
PDB code: 1dor
  9300484 S.Raychaudhuri, F.Younas, P.A.Karplus, C.H.Faerman, and D.R.Ripoll (1997).
Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins.
  Protein Sci, 6, 1849-1857.  
9370345 Y.E.Bruggeman, A.Honegger, H.Kreuwel, A.J.Visser, C.Laane, A.Schots, and R.Hilhorst (1997).
Regulation of the flavin redox potential by flavin-binding antibodies.
  Eur J Biochem, 249, 393-400.  
8706682 A.Belmouden, and F.Lederer (1996).
The role of a beta barrel loop 4 extension in modulating the physical and functional properties of long-chain 2-hydroxy-acid oxidase isozymes.
  Eur J Biochem, 238, 790-798.  
8703001 A.J.Fisher, T.B.Thompson, J.B.Thoden, T.O.Baldwin, and I.Rayment (1996).
The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions.
  J Biol Chem, 271, 21956-21968.
PDB code: 1luc
8885832 J.J.Tanner, B.Lei, S.C.Tu, and K.L.Krause (1996).
Flavin reductase P: structure of a dimeric enzyme that reduces flavin.
  Biochemistry, 35, 13531-13539.
PDB code: 1bkj
8910450 K.Yorita, K.Aki, T.Ohkuma-Soyejima, T.Kokubo, H.Misaki, and V.Massey (1996).
Conversion of L-lactate oxidase to a long chain alpha-hydroxyacid oxidase by site-directed mutagenesis of alanine 95 to glycine.
  J Biol Chem, 271, 28300-28305.  
18626962 M.Devchand, N.Skipper, D.L.Anton, R.Dicosimo, and J.E.Gavagan (1996).
Expression of active spinach glycolate oxidase in Aspergillus nidulans.
  Biotechnol Bioeng, 50, 341-346.  
  8762144 S.Janecek (1996).
Invariant glycines and prolines flanking in loops the strand beta 2 of various (alpha/beta)8-barrel enzymes: a hidden homology?
  Protein Sci, 5, 1136-1143.  
7601095 J.T.Horng, R.Behari, L.E.Burke, and A.Baker (1995).
Investigation of the energy requirement and targeting signal for the import of glycolate oxidase into glyoxysomes.
  Eur J Biochem, 230, 157-163.  
7705356 K.Stenberg, T.Clausen, Y.Lindqvist, and P.Macheroux (1995).
Involvement of Tyr24 and Trp108 in substrate binding and substrate specificity of glycolate oxidase.
  Eur J Biochem, 228, 408-416.
PDB code: 1gyl
  7757015 P.Bork, J.Gellerich, H.Groth, R.Hooft, and F.Martin (1995).
Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search.
  Protein Sci, 4, 268-274.  
  7549888 S.Janecek (1995).
Similarity of different beta-strands flanked in loops by glycines and prolines from distinct (alpha/beta)8-barrel enzymes: chance or a homology?
  Protein Sci, 4, 1239-1242.  
8749369 T.O.Baldwin, J.A.Christopher, F.M.Raushel, J.F.Sinclair, M.M.Ziegler, A.J.Fisher, and I.Rayment (1995).
Structure of bacterial luciferase.
  Curr Opin Struct Biol, 5, 798-809.  
  7849604 A.R.Raine, N.S.Scrutton, and F.S.Mathews (1994).
On the evolution of alternate core packing in eightfold beta/alpha-barrels.
  Protein Sci, 3, 1889-1892.  
8000856 J.E.Seip, S.K.Fager, J.E.Gavagan, D.L.Anton, and R.Di Cosimo (1994).
Glyoxylic acid production using immobilized glycolate oxidase and catalase.
  Bioorg Med Chem, 2, 371-378.  
7881908 K.M.Fox, and P.A.Karplus (1994).
Old yellow enzyme at 2 A resolution: overall structure, ligand binding, and comparison with related flavoproteins.
  Structure, 2, 1089-1105.
PDB codes: 1oya 1oyb 1oyc
7876898 P.L.Chau, and P.M.Dean (1994).
Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects.
  J Comput Aided Mol Des, 8, 513-525.  
7876899 P.L.Chau, and P.M.Dean (1994).
Electrostatic complementarity between proteins and ligands. 2. Ligand moieties.
  J Comput Aided Mol Des, 8, 527-544.  
  7703838 S.A.Moore, and M.N.James (1994).
Common structural features of the luxF protein and the subunits of bacterial luciferase: evidence for a (beta alpha)8 fold in luciferase.
  Protein Sci, 3, 1914-1926.  
8508789 A.Belmouden, K.H.Lê, F.Lederer, and H.J.Garchon (1993).
Molecular cloning and nucleotide sequence of cDNA encoding rat kidney long-chain L-2-hydroxy acid oxidase. Expression of the catalytically active recombinant protein as a chimaera.
  Eur J Biochem, 214, 17-25.  
  8298460 C.C.Correll, M.L.Ludwig, C.M.Bruns, and P.A.Karplus (1993).
Structural prototypes for an extended family of flavoprotein reductases: comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin.
  Protein Sci, 2, 2112-2133.  
  8407843 J.M.Dong, J.S.Taylor, D.J.Latour, S.Iuchi, and E.C.Lin (1993).
Three overlapping lct genes involved in L-lactate utilization by Escherichia coli.
  J Bacteriol, 175, 6671-6678.  
8433995 M.Wilmanns, and D.Eisenberg (1993).
Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold.
  Proc Natl Acad Sci U S A, 90, 1379-1383.  
8504801 P.Macheroux, V.Kieweg, V.Massey, E.Söderlind, K.Stenberg, and Y.Lindqvist (1993).
Role of tyrosine 129 in the active site of spinach glycolate oxidase.
  Eur J Biochem, 213, 1047-1054.  
8141995 S.Janecek, and S.Baláz (1993).
Evolution of parallel beta/alpha-barrel enzyme family lightened by structural data on starch-processing enzymes.
  J Protein Chem, 12, 509-514.  
8378335 Y.M.Chook, H.Ke, and W.N.Lipscomb (1993).
Crystal structures of the monofunctional chorismate mutase from Bacillus subtilis and its complex with a transition state analog.
  Proc Natl Acad Sci U S A, 90, 8600-8603.
PDB codes: 2chs 2cht
  1338973 F.Lederer (1992).
Extreme pKa displacements at the active sites of FMN-dependent alpha-hydroxy acid-oxidizing enzymes.
  Protein Sci, 1, 540-548.  
1470679 J.E.Walker (1992).
The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains.
  Q Rev Biophys, 25, 253-324.  
  1303752 M.E.Karpen, P.L.de Haseth, and K.E.Neet (1992).
Differences in the amino acid distributions of 3(10)-helices and alpha-helices.
  Protein Sci, 1, 1333-1342.  
  1304881 R.Urfer, and K.Kirschner (1992).
The importance of surface loops for stabilizing an eightfold beta alpha barrel protein.
  Protein Sci, 1, 31-45.  
1709492 H.Nakamura, K.Katayanagi, K.Morikawa, and M.Ikehara (1991).
Structural models of ribonuclease H domains in reverse transcriptases from retroviruses.
  Nucleic Acids Res, 19, 1817-1823.  
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.