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(-) Description

Title :  CRYSTAL STRUCTURE OF CHOLESTEROL OXIDASE FROM B.STEROLICUM
 
Authors :  R. Coulombe, K. Q. Yue, S. Ghisla, A. Vrielink
Date :  31 Jan 01  (Deposition) - 08 Aug 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mix Alpha Beta, Covalent Fad, Flavoenzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Coulombe, K. Q. Yue, S. Ghisla, A. Vrielink
Oxygen Access To The Active Site Of Cholesterol Oxidase Through A Narrow Channel Is Gated By An Arg-Glu Pair.
J. Biol. Chem. V. 276 30435 2001
PubMed-ID: 11397813  |  Reference-DOI: 10.1074/JBC.M104103200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHOLESTEROL OXIDASE
    Chains: A, B
    EC Number: 1.1.3.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BREVIBACTERIUM STEROLICUM
    Organism Taxid: 1702
    Other Details: COVALENT FAD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2EDO12Ligand/Ion1,2-ETHANEDIOL
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MN3Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CAC-1Ligand/IonCACODYLATE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN B:542 , GLU B:579 , CAC B:703 , HOH B:1862 , HOH B:1863 , HOH B:1872BINDING SITE FOR RESIDUE MN B 702
02AC2SOFTWAREHIS A:108 , GLU A:109 , ASP A:111 , HOH A:1193 , ASN B:542 , ASN B:543 , GLU B:579 , MN B:702BINDING SITE FOR RESIDUE CAC B 703
03AC3SOFTWAREHOH B:1480 , HOH B:1875 , HOH B:1898 , HOH B:1924 , HOH B:1925BINDING SITE FOR RESIDUE MN B 704
04AC4SOFTWAREASP B:545 , HOH B:1984 , HOH B:1985 , HOH B:1986BINDING SITE FOR RESIDUE MN B 705
05AC5SOFTWAREILE A:423 , GLU A:432 , GLU A:475 , ARG A:477 , LYS A:554 , FAD A:700 , HOH A:1001 , HOH A:1002 , EDO A:3002BINDING SITE FOR RESIDUE EDO A 3001
06AC6SOFTWARETRP A:123 , ILE A:423 , LEU A:430 , GLU A:432 , LEU A:518 , EDO A:3001BINDING SITE FOR RESIDUE EDO A 3002
07AC7SOFTWAREPRO A:125 , GLU A:129 , TYR A:563 , HOH A:1382 , HOH A:1825BINDING SITE FOR RESIDUE EDO A 3003
08AC8SOFTWAREGLU A:83 , PRO A:562 , TYR A:563 , HOH A:1293 , HOH A:1362 , HOH A:1382 , HOH A:2001BINDING SITE FOR RESIDUE EDO A 3004
09AC9SOFTWAREASN A:595 , PRO A:599 , ARG A:601 , PRO A:613 , THR B:446 , ASP B:450BINDING SITE FOR RESIDUE EDO A 3005
10BC1SOFTWAREILE B:423 , GLU B:432 , GLU B:475 , ARG B:477 , ASN B:516 , LYS B:554 , FAD B:701 , HOH B:1004BINDING SITE FOR RESIDUE EDO B 3011
11BC2SOFTWARETRP B:123 , ILE B:423 , LEU B:430 , GLU B:432 , LEU B:518BINDING SITE FOR RESIDUE EDO B 3012
12BC3SOFTWAREPRO B:125 , GLU B:129 , TYR B:563 , PHE B:607 , HOH B:1320 , HOH B:1520 , HOH B:1958BINDING SITE FOR RESIDUE EDO B 3013
13BC4SOFTWAREHOH A:1629 , ILE B:578 , GLU B:579 , GLY B:580 , VAL B:581 , HOH B:1343BINDING SITE FOR RESIDUE EDO B 3014
14BC5SOFTWARELEU B:241 , GLU B:242 , THR B:243 , HOH B:1990BINDING SITE FOR RESIDUE EDO B 3015
15BC6SOFTWAREARG B:441 , ASP B:510 , HOH B:1518 , HOH B:1822BINDING SITE FOR RESIDUE EDO B 3016
16BC7SOFTWAREILE B:84 , PRO B:562 , HOH B:1207 , HOH B:1300 , HOH B:1320 , HOH B:1465BINDING SITE FOR RESIDUE EDO B 3017
17BC8SOFTWARETRP A:80 , ARG A:115 , PRO A:116 , GLY A:118 , ALA A:119 , MET A:120 , HIS A:121 , GLY A:122 , TRP A:123 , LEU A:126 , ALA A:164 , PRO A:186 , ALA A:187 , PRO A:188 , LEU A:191 , SER A:192 , GLY A:194 , GLY A:195 , ALA A:198 , ALA A:201 , HIS A:202 , ASN A:257 , LEU A:258 , GLY A:259 , CYS A:261 , LEU A:263 , ARG A:477 , HOH A:1002 , HOH A:1006 , HOH A:1027 , HOH A:1033 , HOH A:1039 , HOH A:1047 , HOH A:1055 , HOH A:1072 , EDO A:3001BINDING SITE FOR RESIDUE FAD A 700
18BC9SOFTWARETRP B:80 , ARG B:115 , PRO B:116 , GLY B:118 , ALA B:119 , MET B:120 , HIS B:121 , GLY B:122 , TRP B:123 , LEU B:126 , ALA B:164 , PRO B:186 , ALA B:187 , PRO B:188 , LEU B:191 , SER B:192 , GLY B:194 , GLY B:195 , ALA B:198 , VAL B:199 , ALA B:201 , HIS B:202 , LEU B:258 , GLY B:259 , CYS B:261 , LEU B:263 , ARG B:477 , HOH B:1003 , HOH B:1089 , HOH B:1110 , HOH B:1116 , HOH B:1122 , HOH B:1130 , HOH B:1138 , HOH B:1153 , EDO B:3011BINDING SITE FOR RESIDUE FAD B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I19)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:559 -Pro A:560
2Gly B:559 -Pro B:560

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I19)

(-) Exons   (0, 0)

(no "Exon" information available for 1I19)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:541
 aligned with Q7SID9_BREST | Q7SID9 from UniProtKB/TrEMBL  Length:561

    Alignment length:557
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       
         Q7SID9_BREST     5 VAPLPTPPNFPNDIALFQQAYQNWSKEIMLDATWVCSPKTPQDVVRLANWAHEHDYKIRPRGAMHGWTPLTVEKGANVEKVILADTMTHLNGITVNTGGPVATVTAGAGASIEAIVTELQKHDLGWANLPAPGVLSIGGALAVNAHGAALPAVGQTTLPGHTYGSLSNLVTELTAVVWNGTTYALETYQRNDPRITPLLTNLGRCFLTSVTMQAGPNFRQRCQSYTDIPWRELFAPKGADGRTFEKFVAESGGAEAIWYPFTEKPWMKVWTVSPTKPDSSNEVGSLGSAGSLVGKPPQAREVSGPYNYIFSDNLPEPITDMIGAINAGNPGIAPLFGPAMYEITKLGLAATNANDIWGWSKDVQFYIKATTLRLTEGGGAVVTSRANIATVINDFTEWFHERIEFYRAKGEFPLNGPVEIRCCGLDQAADVKVPSVGPPTISATRPRPDHPDWDVAIWLNVLGVPGTPGMFEFYREMEQWMRSHYNNDDATFRPEWSKGWAFGPDPYTDNDIVTNKMRATYIEGVPTTENWDTARARYNQIDPHRVFTNGFMDKLLP 561
               SCOP domains d1i19a2 A:57-273 Cholesterol oxidase                                                                                                                                                                                     d1i19a1 A:274-613 Cholesterol oxidase                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------1i19A01 A:71-146                                                            1i19A02 A:147-272  [code=3.30.465.10, no name defined]                                                                        1i19A03 A:273-563 Vanillyl-alcohol Oxidase; Chain A, domai                n 3                                                                                                                                                                                                                      1i19A04 A:564-613                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeee......eeeeeeee...hhhhhhhhhhhhhhh..eeeee...................eeeee.......eeee......eeeee...hhhhhhhhhhhh.ee..........hhhhhhhh.....................hhhh.eeeeeeeee....eeeeeee.....hhhhh.......eeeeeee.ee..eeeeeee...hhhhhh........hhhhhhhhhheeeeee.......eeeeeee..----------------.........ee.............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.........eeeeee...hhhhh.......................eeeeeeeee.....hhhhhhhhhhhhhhhhh....eeee...............hhhhhhhhhhhhh........hhhhhhhhhhhhh......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i19 A  57 VAPLPTPPNFPNDIALFQQAYQNWSKEIMLDATWVCSPKTPQDVVRLANWAHEHDYKIRPRGAMHGWTPLTVEKGANVEKVILADTMTHLNGITVNTGGPVATVTAGAGASIEAIVTELQKHDLGWANLPAPGVLSIGGALAVNAHGAALPAVGQTTLPGHTYGSLSNLVTELTAVVWNGTTYALETYQRNDPRITPLLTNLGRCFLTSVTMQAGPNFRQRCQSYTDIPWRELFAPKGADGRTFEKFVAESGGAEAIWYPFTEKPWMKVWTVSP----------------SLVGKPPQAREVSGPYNYIFSDNLPEPITDMIGAINAGNPGIAPLFGPAMYEITKLGLAATNANDIWGWSKDVQFYIKATTLRLTEGGGAVVTSRANIATVINDFTEWFHERIEFYRAKGEFPLNGPVEIRCCGLDQAADVKVPSVGPPTISATRPRPDHPDWDVAIWLNVLGVPGTPGMFEFYREMEQWMRSHYNNDDATFRPEWSKGWAFGPDPYTDNDIVTNKMRATYIEGVPTTENWDTARARYNQIDPHRVFTNGFMDKLLP 613
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326   |     -         -|      356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       
                                                                                                                                                                                                                                                                                                           330              347                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:538
 aligned with Q7SID9_BREST | Q7SID9 from UniProtKB/TrEMBL  Length:561

    Alignment length:557
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       
         Q7SID9_BREST     5 VAPLPTPPNFPNDIALFQQAYQNWSKEIMLDATWVCSPKTPQDVVRLANWAHEHDYKIRPRGAMHGWTPLTVEKGANVEKVILADTMTHLNGITVNTGGPVATVTAGAGASIEAIVTELQKHDLGWANLPAPGVLSIGGALAVNAHGAALPAVGQTTLPGHTYGSLSNLVTELTAVVWNGTTYALETYQRNDPRITPLLTNLGRCFLTSVTMQAGPNFRQRCQSYTDIPWRELFAPKGADGRTFEKFVAESGGAEAIWYPFTEKPWMKVWTVSPTKPDSSNEVGSLGSAGSLVGKPPQAREVSGPYNYIFSDNLPEPITDMIGAINAGNPGIAPLFGPAMYEITKLGLAATNANDIWGWSKDVQFYIKATTLRLTEGGGAVVTSRANIATVINDFTEWFHERIEFYRAKGEFPLNGPVEIRCCGLDQAADVKVPSVGPPTISATRPRPDHPDWDVAIWLNVLGVPGTPGMFEFYREMEQWMRSHYNNDDATFRPEWSKGWAFGPDPYTDNDIVTNKMRATYIEGVPTTENWDTARARYNQIDPHRVFTNGFMDKLLP 561
               SCOP domains d1i19b2 B:57-273 Cholesterol oxidase                                                                                                                                                                                     d1i19b1 B:274-613 Cholesterol oxidase                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------1i19B01 B:71-146                                                            1i19B02 B:147-272  [code=3.30.465.10, no name defined]                                                                        1i19B03 B:273-563 Vanillyl-alcohol Oxidase; Chain A, doma                   in 3                                                                                                                                                                                                                   1i19B04 B:564-613                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeee......eeeeeeee...hhhhhhhhhhhhhhhh.eeeee...................eeeee.......eeee.....eeeeee...hhhhhhhhhhh..ee..........hhhhhhhh.....................hhhh.eeeeeeeee....eeeeeee.....hhhhh.......eeeeeeeeee..eeeeeee...hhhhhh........hhhhhhhhhheeeeee.......eeeeeee.-------------------.......ee......hhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh........eeeeee...hhhhh.......................eeeeeeeee.....hhhhhhhhhhhhhhhhh....eeee...............hhhhhhhhhhhhh........hhhhhhhhhhhhh......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i19 B  57 VAPLPTPPNFPNDIALFQQAYQNWSKEIMLDATWVCSPKTPQDVVRLANWAHEHDYKIRPRGAMHGWTPLTVEKGANVEKVILADTMTHLNGITVNTGGPVATVTAGAGASIEAIVTELQKHDLGWANLPAPGVLSIGGALAVNAHGAALPAVGQTTLPGHTYGSLSNLVTELTAVVWNGTTYALETYQRNDPRITPLLTNLGRCFLTSVTMQAGPNFRQRCQSYTDIPWRELFAPKGADGRTFEKFVAESGGAEAIWYPFTEKPWMKVWTVS-------------------VGKPPQAREVSGPYNYIFSDNLPEPITDMIGAINAGNPGIAPLFGPAMYEITKLGLAATNANDIWGWSKDVQFYIKATTLRLTEGGGAVVTSRANIATVINDFTEWFHERIEFYRAKGEFPLNGPVEIRCCGLDQAADVKVPSVGPPTISATRPRPDHPDWDVAIWLNVLGVPGTPGMFEFYREMEQWMRSHYNNDDATFRPEWSKGWAFGPDPYTDNDIVTNKMRATYIEGVPTTENWDTARARYNQIDPHRVFTNGFMDKLLP 613
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326  |      -         -  |    356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       
                                                                                                                                                                                                                                                                                                          329                 349
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (4, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I19)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7SID9_BREST | Q7SID9)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  1i19
    Family and Domain Information: ProDom | SYSTERS
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  Q7SID9_BREST | Q7SID9
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  1.1.3.6
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q7SID9_BREST | Q7SID9: 2i0k

(-) Related Entries Specified in the PDB File

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