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PDBsum entry 3cox

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protein ligands links
Oxidoreductase(oxygen receptor) PDB id
3cox
Jmol
Contents
Protein chain
500 a.a. *
Ligands
FAD
Waters ×453
* Residue conservation analysis
PDB id:
3cox
Name: Oxidoreductase(oxygen receptor)
Title: Crystal structure of cholesterol oxidase complexed with a steroid substrate. Implications for fad dependent alcohol oxidases
Structure: Cholesterol oxidase. Chain: a. Engineered: yes
Source: Brevibacterium sterolicum. Organism_taxid: 1702
Resolution:
1.80Å     R-factor:   0.156    
Authors: A.Vrielink,J.Li,P.Brick,D.M.Blow
Key ref:
J.Li et al. (1993). Crystal structure of cholesterol oxidase complexed with a steroid substrate: implications for flavin adenine dinucleotide dependent alcohol oxidases. Biochemistry, 32, 11507-11515. PubMed id: 8218217 DOI: 10.1021/bi00094a006
Date:
14-Jun-93     Release date:   31-Oct-93    
Supersedes: 1cox
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22637  (CHOD_BREST) -  Cholesterol oxidase
Seq:
Struc:
 
Seq:
Struc:
552 a.a.
500 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: E.C.1.1.3.6  - Cholesterol oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cholesterol + O2 = cholest-5-en-3-one + H2O2
Cholesterol
+ O(2)
= cholest-5-en-3-one
+ H(2)O(2)
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
   Enzyme class 3: E.C.5.3.3.1  - Steroid Delta-isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A 3-oxo-Delta5-steroid = a 3-oxo-Delta4-steroid
3-oxo-Delta(5)-steroid
= 3-oxo-Delta(4)-steroid
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     extracellular region   1 term 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi00094a006 Biochemistry 32:11507-11515 (1993)
PubMed id: 8218217  
 
 
Crystal structure of cholesterol oxidase complexed with a steroid substrate: implications for flavin adenine dinucleotide dependent alcohol oxidases.
J.Li, A.Vrielink, P.Brick, D.M.Blow.
 
  ABSTRACT  
 
Cholesterol oxidase from Brevibacterium sterolicum is a flavin-dependent enzyme that catalyzes the oxidation and isomerization of 3 beta-hydroxy steroids with a double bond at delta 5-delta 6 of the steroid ring backbone. The crystal structure of the free enzyme in the absence of a steroid substrate has previously been determined. In this paper we report the crystal structure of the complex of cholesterol oxidase with the steroid substrate dehydroisoandrosterone, refined at 1.8-A resolution. The final crystallographic R-value is 15.7% for all reflections between 10.0- and 1.8-A resolution. The steroid is buried within the protein in an internal cavity which, in the free enzyme crystal structure, was occupied by a lattice of water molecules. The conformations of a number of side chains lining the active-site cavity have changed in order to accommodate the steroid substrate. A loop region of the structure between residues 70 and 90 differs significantly between the substrate-free and substrate-bound forms of the enzyme, presumably to facilitate binding of the steroid. The hydroxyl group of the steroid substrate is hydrogen-bonded to both the flavin ring system of the FAD cofactor and a bound water molecule. FAD-dependent cholesterol oxidase shares significant structural homology with another flavoenzyme, glucose oxidase, suggesting that it might also be a member of the glucose-methanol-choline (GMC) oxidoreductase family. Although there is only limited sequence homology, a superposition of these two structures reveals a conserved histidine residue within hydrogen-bonding distance of the active-site water molecule.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20467737 D.Ribitsch, S.Winkler, K.Gruber, W.Karl, E.Wehrschütz-Sigl, I.Eiteljörg, P.Schratl, P.Remler, R.Stehr, C.Bessler, N.Mussmann, K.Sauter, K.H.Maurer, and H.Schwab (2010).
Engineering of choline oxidase from Arthrobacter nicotianae for potential use as biological bleach in detergents.
  Appl Microbiol Biotechnol, 87, 1743-1752.  
19256550 I.Dreveny, A.S.Andryushkova, A.Glieder, K.Gruber, and C.Kratky (2009).
Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity.
  Biochemistry, 48, 3370-3377.
PDB codes: 3gdn 3gdp
19843168 J.Kreit, and N.S.Sampson (2009).
Cholesterol oxidase: physiological functions.
  FEBS J, 276, 6844-6856.  
19495743 N.Doukyu (2009).
Characteristics and biotechnological applications of microbial cholesterol oxidases.
  Appl Microbiol Biotechnol, 83, 825-837.  
19129502 T.H.Scheuermann, D.R.Tomchick, M.Machius, Y.Guo, R.K.Bruick, and K.H.Gardner (2009).
Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor.
  Proc Natl Acad Sci U S A, 106, 450-455.
PDB codes: 3f1n 3f1o 3f1p
19243237 T.Senda, M.Senda, S.Kimura, and T.Ishida (2009).
Redox control of protein conformation in flavoproteins.
  Antioxid Redox Signal, 11, 1741-1766.  
18482980 C.Michalski, H.Mohagheghi, M.Nimtz, J.Pasteels, and D.Ober (2008).
Salicyl alcohol oxidase of the chemical defense secretion of two chrysomelid leaf beetles. Molecular and functional characterization of two new members of the glucose-methanol-choline oxidoreductase gene family.
  J Biol Chem, 283, 19219-19228.  
18633481 J.F.Aparicio, and J.F.Martín (2008).
Microbial cholesterol oxidases: bioconversion enzymes or signal proteins?
  Mol Biosyst, 4, 804-809.  
18614534 L.Piubelli, M.Pedotti, G.Molla, S.Feindler-Boeckh, S.Ghisla, M.S.Pilone, and L.Pollegioni (2008).
On the Oxygen Reactivity of Flavoprotein Oxidases: AN OXYGEN ACCESS TUNNEL AND GATE IN BREVIBACTERIUM STEROLICUM CHOLESTEROL OXIDASE.
  J Biol Chem, 283, 24738-24747.  
18039763 Y.R.Chiang, W.Ismail, D.Heintz, C.Schaeffer, A.Van Dorsselaer, and G.Fuchs (2008).
Study of anoxic and oxic cholesterol metabolism by Sterolibacterium denitrificans.
  J Bacteriol, 190, 905-914.  
18029419 A.Y.Lyubimov, K.Heard, H.Tang, N.S.Sampson, and A.Vrielink (2007).
Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase.
  Protein Sci, 16, 2647-2656.
PDB codes: 3b3r 3b6d
17668316 G.Gimpl, and K.Gehrig-Burger (2007).
Cholesterol reporter molecules.
  Biosci Rep, 27, 335-358.  
17307741 Y.R.Chiang, W.Ismail, M.Müller, and G.Fuchs (2007).
Initial steps in the anoxic metabolism of cholesterol by the denitrifying Sterolibacterium denitrificans.
  J Biol Chem, 282, 13240-13249.  
16999821 P.Ferreira, F.J.Ruiz-Dueñas, M.J.Martínez, W.J.van Berkel, and A.T.Martínez (2006).
Site-directed mutagenesis of selected residues at the active site of aryl-alcohol oxidase, an H2O2-producing ligninolytic enzyme.
  FEBS J, 273, 4878-4888.  
15819891 Y.S.Yun, G.H.Nam, Y.G.Kim, B.H.Oh, and K.Y.Choi (2005).
Small exterior hydrophobic cluster contributes to conformational stability and steroid binding in ketosteroid isomerase from Pseudomonas putida biotype B.
  FEBS J, 272, 1999-2011.
PDB code: 1w6y
12493734 B.M.Hallberg, G.Henriksson, G.Pettersson, A.Vasella, and C.Divne (2003).
Mechanism of the reductive half-reaction in cellobiose dehydrogenase.
  J Biol Chem, 278, 7160-7166.
PDB code: 1naa
14690428 M.Ghanem, F.Fan, K.Francis, and G.Gadda (2003).
Spectroscopic and kinetic properties of recombinant choline oxidase from Arthrobacter globiformis.
  Biochemistry, 42, 15179-15188.  
12843070 N.Ladrón, M.Fernández, J.Agüero, B.González Zörn, J.A.Vázquez-Boland, and J.Navas (2003).
Rapid identification of Rhodococcus equi by a PCR assay targeting the choE gene.
  J Clin Microbiol, 41, 3241-3245.  
12623022 Y.An, Y.Shao, C.Alory, J.Matteson, T.Sakisaka, W.Chen, R.A.Gibbs, I.A.Wilson, and W.E.Balch (2003).
Geranylgeranyl switching regulates GDI-Rab GTPase recycling.
  Structure, 11, 347-357.
PDB code: 1lv0
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.  
11790839 I.Dreveny, C.Kratky, and K.Gruber (2002).
The active site of hydroxynitrile lyase from Prunus amygdalus: modeling studies provide new insights into the mechanism of cyanogenesis.
  Protein Sci, 11, 292-300.  
11761324 C.J.Rizzo (2001).
Further computational studies on the conformation of 1,5-dihydrolumiflavin.
  Antioxid Redox Signal, 3, 737-746.  
11135412 J.F.Biellmann (2001).
Resolution of alcohols by cholesterol oxidase fromRrhodococcus erythropolis: lack of enantiospecificity for the steroids.
  Chirality, 13, 34-39.  
11761331 N.S.Sampson (2001).
Dissection of a flavoenzyme active site: the reaction catalyzed by cholesterol oxidase.
  Antioxid Redox Signal, 3, 839-846.  
11463661 S.Weber, G.Richter, E.Schleicher, A.Bacher, K.Möbius, and C.W.Kay (2001).
Substrate binding to DNA photolyase studied by electron paramagnetic resonance spectroscopy.
  Biophys J, 81, 1195-1204.  
16233019 Y.Murooka, and M.Yamashita (2001).
Genetic and protein engineering of diagnostic enzymes, cholesterol oxidase and xylitol oxidase.
  J Biosci Bioeng, 91, 433-441.  
10962107 E.Varela, M.Jesús Martínez, and A.T.Martínez (2000).
Aryl-alcohol oxidase protein sequence: a comparison with glucose oxidase and other FAD oxidoreductases.
  Biochim Biophys Acta, 1481, 202-208.
PDB code: 1qjn
10651042 O.Vallon (2000).
New sequence motifs in flavoproteins: evidence for common ancestry and tools to predict structure.
  Proteins, 38, 95.  
11063575 X.Chen, D.E.Wolfgang, and N.S.Sampson (2000).
Use of the parallax-quench method to determine the position of the active-site loop of cholesterol oxidase in lipid bilayers.
  Biochemistry, 39, 13383-13389.  
10216293 G.Wohlfahrt, S.Witt, J.Hendle, D.Schomburg, H.M.Kalisz, and H.J.Hecht (1999).
1.8 and 1.9 A resolution structures of the Penicillium amagasakiense and Aspergillus niger glucose oxidases as a basis for modelling substrate complexes.
  Acta Crystallogr D Biol Crystallogr, 55, 969-977.
PDB codes: 1cf3 1gpe
10447682 L.Pollegioni, G.Wels, M.S.Pilone, and S.Ghisla (1999).
Kinetic mechanisms of cholesterol oxidase from Streptomyces hygroscopicus and Brevibacterium sterolicum.
  Eur J Biochem, 264, 140-151.  
10368302 P.Trickey, M.A.Wagner, M.S.Jorns, and F.S.Mathews (1999).
Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.
  Structure, 7, 331-345.
PDB codes: 1b3m 1l9f 2gb0
10194345 Q.K.Yue, I.J.Kass, N.S.Sampson, and A.Vrielink (1999).
Crystal structure determination of cholesterol oxidase from Streptomyces and structural characterization of key active site mutants.
  Biochemistry, 38, 4277-4286.
PDB codes: 1b4v 1b8s 1cbo 1cc2
10509900 Y.Nishiya, and N.Hirayama (1999).
Alteration of substrate affinity of Streptomyces cholesterol oxidase for application to the rate assay of cholesterol in serum.
  Clin Chim Acta, 287, 111-122.  
9546198 A.Mattevi (1998).
The PHBH fold: not only flavoenzymes.
  Biophys Chem, 70, 217-222.  
9634698 C.Enroth, H.Neujahr, G.Schneider, and Y.Lindqvist (1998).
The crystal structure of phenol hydroxylase in complex with FAD and phenol provides evidence for a concerted conformational change in the enzyme and its cofactor during catalysis.
  Structure, 6, 605-617.
PDB code: 1foh
9726992 D.Parsonage, J.Luba, T.C.Mallett, and A.Claiborne (1998).
The soluble alpha-glycerophosphate oxidase from Enterococcus casseliflavus. Sequence homology with the membrane-associated dehydrogenase and kinetic analysis of the recombinant enzyme.
  J Biol Chem, 273, 23812-23822.  
9558355 G.Gadda, and P.F.Fitzpatrick (1998).
Biochemical and physical characterization of the active FAD-containing form of nitroalkane oxidase from Fusarium oxysporum.
  Biochemistry, 37, 6154-6164.  
9922167 I.J.Kass, and N.S.Sampson (1998).
Evaluation of the role of His447 in the reaction catalyzed by cholesterol oxidase.
  Biochemistry, 37, 17990-18000.  
9425157 M.Vashishtha, T.Phalen, M.T.Marquardt, J.S.Ryu, A.C.Ng, and M.Kielian (1998).
A single point mutation controls the cholesterol dependence of Semliki Forest virus entry and exit.
  J Cell Biol, 140, 91-99.  
9548964 N.S.Sampson, I.J.Kass, and K.B.Ghoshroy (1998).
Assessment of the role of an omega loop of cholesterol oxidase: a truncated loop mutant has altered substrate specificity.
  Biochemistry, 37, 5770-5778.  
9434899 A.Mattevi, M.A.Vanoni, and B.Curti (1997).
Structure of D-amino acid oxidase: new insights from an old enzyme.
  Curr Opin Struct Biol, 7, 804-810.  
9261083 A.Mattevi, M.W.Fraaije, A.Mozzarelli, L.Olivi, A.Coda, and W.J.van Berkel (1997).
Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity.
  Structure, 5, 907-920.
PDB codes: 1ahu 1ahv 1ahz 1vao 2vao
9428686 G.Gadda, G.Wels, L.Pollegioni, S.Zucchelli, D.Ambrosius, M.S.Pilone, and S.Ghisla (1997).
Characterization of cholesterol oxidase from Streptomyces hygroscopicus and Brevibacterium sterolicum.
  Eur J Biochem, 250, 369-376.  
9038163 G.Gadda, R.D.Edmondson, D.H.Russell, and P.F.Fitzpatrick (1997).
Identification of the naturally occurring flavin of nitroalkane oxidase from fusarium oxysporum as a 5-nitrobutyl-FAD and conversion of the enzyme to the active FAD-containing form.
  J Biol Chem, 272, 5563-5570.  
9166784 K.B.Ghoshroy, W.Zhu, and N.S.Sampson (1997).
Investigation of membrane disruption in the reaction catalyzed by cholesterol oxidase.
  Biochemistry, 36, 6133-6140.  
9218444 M.W.Fraaije, and W.J.van Berkel (1997).
Catalytic mechanism of the oxidative demethylation of 4-(methoxymethyl)phenol by vanillyl-alcohol oxidase. Evidence for formation of a p-quinone methide intermediate.
  J Biol Chem, 272, 18111-18116.  
18634028 P.T.Vasudevan, and T.Zhou (1997).
Enzymatic assay of cholesterol by reaction rate measurements.
  Biotechnol Bioeng, 53, 391-396.  
8755502 A.Mattevi, M.A.Vanoni, F.Todone, M.Rizzi, A.Teplyakov, A.Coda, M.Bolognesi, and B.Curti (1996).
Crystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2.
  Proc Natl Acad Sci U S A, 93, 7496-7501.
PDB code: 1kif
8662689 J.C.Silva, R.E.Minto, C.E.Barry, K.A.Holland, and C.A.Townsend (1996).
Isolation and characterization of the versicolorin B synthase gene from Aspergillus parasiticus. Expansion of the aflatoxin b1 biosynthetic gene cluster.
  J Biol Chem, 271, 13600-13608.  
8727640 L.L.Smith (1996).
Review of progress in sterol oxidations: 1987-1995.
  Lipids, 31, 453-487.  
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.  
8789193 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 2. Influence of local site surface shape on water binding.
  J Comput Aided Mol Des, 9, 513-520.  
8519982 V.Helms, and R.C.Wade (1995).
Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study.
  Biophys J, 69, 810-824.  
8026504 M.Medina, A.Vrielink, and R.Cammack (1994).
ESR and electron nuclear double resonance characterization of the cholesterol oxidase from Brevibacterium sterolicum in its semiquinone state.
  Eur J Biochem, 222, 941-947.  
  7756982 W.J.van Berkel, M.H.Eppink, and H.A.Schreuder (1994).
Crystal structure of p-hydroxybenzoate hydroxylase reconstituted with the modified FAD present in alcohol oxidase from methylotrophic yeasts: evidence for an arabinoflavin.
  Protein Sci, 3, 2245-2253.
PDB code: 1pdh
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.