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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A
 
Authors :  R. A. Steiner
Date :  20 May 09  (Deposition) - 26 Jan 10  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Alpha/Beta Hydrolase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Steiner, H. J. Janssen, P. Roversi, A. J. Oakley, S. Fetzner
Structural Basis For Cofactor-Independent Dioxygenation Of N-Heteroaromatic Compounds At The {Alpha}/{Beta}-Hydrolase Fold.
Proc. Natl. Acad. Sci. Usa V. 107 657 2010
PubMed-ID: 20080731  |  Reference-DOI: 10.1073/PNAS.0909033107
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
    Chains: A, B, C, D
    EC Number: 1.13.11.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M15/PREP4
    Expression System Taxid: 562
    Expression System Vector: PQE30
    Mutation: YES
    Organism Scientific: ARTHROBACTER NITROGUAJACOLICUS
    Organism Taxid: 211146
    Strain: RU61A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SRT8Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SRT2Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SRT2Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SRT2Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SRT2Ligand/IonS,R MESO-TARTARIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:235 , TYR A:243 , ASP D:158BINDING SITE FOR RESIDUE GOL A1276
02AC2SOFTWARESER B:101 , HIS B:102 , ASP B:126 , TRP B:127 , LEU B:128 , PHE B:136 , TRP B:160 , HIS B:251 , HOH B:2026BINDING SITE FOR RESIDUE GOL B1276
03AC3SOFTWARELYS A:167 , ARG A:170 , HIS A:171 , ARG C:260 , VAL C:263BINDING SITE FOR RESIDUE SRT A1277
04AC4SOFTWARELYS B:167 , ARG B:170 , HIS B:171 , ARG D:260 , VAL D:263BINDING SITE FOR RESIDUE SRT B1277
05AC5SOFTWAREARG B:260 , VAL B:263 , LYS C:167 , ARG C:170 , HIS C:171BINDING SITE FOR RESIDUE SRT C1275
06AC6SOFTWAREARG A:260 , VAL A:263 , LYS D:167 , ARG D:170 , HIS D:171BINDING SITE FOR RESIDUE SRT D1275
07AC7SOFTWAREHIS A:164 , ASP A:165 , LYS C:245 , LEU C:246 , GLY C:247 , HOH C:2086 , HOH C:2087 , HOH C:2088BINDING SITE FOR RESIDUE SRT C1276
08AC8SOFTWARELYS B:245 , LEU B:246 , GLY B:247 , HOH B:2069 , HOH B:2070 , HOH B:2071 , GLY C:163 , HIS C:164 , ASP C:165 , GLU C:166BINDING SITE FOR RESIDUE SRT B1278
09AC9SOFTWAREHIS B:164 , ASP B:165 , HOH B:2040 , LYS D:245 , LEU D:246 , GLY D:247 , HOH D:2055 , HOH D:2056BINDING SITE FOR RESIDUE SRT D1276
10BC1SOFTWARELYS A:245 , LEU A:246 , GLY A:247 , HOH A:2064 , HIS D:164 , ASP D:165 , GLU D:166BINDING SITE FOR RESIDUE SRT A1278

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:37 -A:184
2B:37 -B:184
3C:37 -C:184
4D:37 -D:184

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:27 -Pro A:28
2Gln A:221 -Pro A:222
3Gly B:27 -Pro B:28
4Gln B:221 -Pro B:222
5Gly C:27 -Pro C:28
6Gln C:221 -Pro C:222
7Gly D:27 -Pro D:28
8Gln D:221 -Pro D:222

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WJ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WJ3)

(-) Exons   (0, 0)

(no "Exon" information available for 2WJ3)

(-) 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:274
 aligned with HOD_PAENT | O31266 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
            HOD_PAENT     2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPCEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQG 275
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeee..eeeeeee........eeeee.....hhhhhhhhhhhhh....eeee...............hhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wj3 A   2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPSEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQG 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    


Chain B from PDB  Type:PROTEIN  Length:273
 aligned with HOD_PAENT | O31266 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:273
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   
            HOD_PAENT     3 DTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPCEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQG 275
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeeee........eeeee.....hhhhhhhhhhhhh....eeee...............hhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wj3 B   3 DTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPSEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQG 275
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   


Chain C from PDB  Type:PROTEIN  Length:273
 aligned with HOD_PAENT | O31266 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:273
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   
            HOD_PAENT     2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPCEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQ 274
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeee..eeeeeee........eeeee.....hhhhhhhhhhhhh....eeee...............hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wj3 C   2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPSEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQ 274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   


Chain D from PDB  Type:PROTEIN  Length:273
 aligned with HOD_PAENT | O31266 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:273
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   
            HOD_PAENT     2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPCEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQ 274
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeee........eeeee.....hhhhhhhhhhhhh....eeee...............hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wj3 D   2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPSEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQ 274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2WJ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WJ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WJ3)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (HOD_PAENT | O31266)
molecular function
    GO:0050586    3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity    Catalysis of the reaction: 3-hydroxy-2-methylquinolin-4(1H)-one + H(+) + O(2) = N-acetylanthranilate + CO.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    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:0016702    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    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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  2wj3
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  HOD_PAENT | O31266
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 Related Entries

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

UniProtKB/Swiss-Prot
        HOD_PAENT | O31266: 2wj4 2wj6 2wm2 4cfs

(-) Related Entries Specified in the PDB File

2wj4 CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1- H-3-HYDROXY-4-OXOQUINALDINE 2,4- DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A ANAEROBICALLY COMPLEXED WITH ITS NATURAL SUBSTRATE 1-H-3-HYDROXY- 4-OXOQUINALDINE
2wj6 CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1- H-3-HYDROXY-4-OXOQUINALDINE 2,4- DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A COMPLEXED WITH ITS NATURAL SUBSTRATE N-ACETYLANTHRANILATE
2wm2 CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1- H-3-HYDROXY-4-OXOQUINALDINE 2,4- DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A IN COMPLEX WITH CHLORIDE