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(-) Description

Title :  CRYSTAL STRUCTURE OF NATIVE 1,6-APD (2-ANIMOPHENOL-1,6-DIOXYGENASE) COMPLEX WITH 4-NITROCATECHOL
 
Authors :  D. F. Li, Y. J. Hou, Y. Hu, D. C. Wang, W. Liu
Date :  25 Apr 12  (Deposition) - 16 Jan 13  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Extradiol Dioxygenase, Cnbc, 2-His-1-Carboxylate Facial Triad Motif, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. F. Li, J. Y. Zhang, Y. J. Hou, L. Liu, Y. Hu, S. J. Liu, D. C. Wang, W. Liu
Structures Of Aminophenol Dioxygenase In Complex With Intermediate, Product And Inhibitor
Acta Crystallogr. , Sect. D V. 69 32 2013
PubMed-ID: 23275161  |  Reference-DOI: 10.1107/S0907444912042072

(-) Compounds

Molecule 1 - 2-AMINO-5-CHLOROPHENOL 1,6-DIOXYGENASE ALPHA SUBUNIT
    Chains: A, C
    EC Number: 1.13.11.8
    Organism Scientific: COMAMONAS TESTOSTERONI
    Organism Taxid: 543891
    Strain: CNB-1
 
Molecule 2 - 2-AMINO-5-CHLOROPHENOL 1,6-DIOXYGENASE BETA SUBUNIT
    Chains: B, D
    EC Number: 1.13.11.8
    Organism Scientific: COMAMONAS TESTOSTERONI
    Organism Taxid: 543891
    Strain: CNB-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
14NC2Ligand/Ion4-NITROCATECHOL
2FE2Ligand/IonFE (III) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:13 , HIS B:62 , GLU B:251 , 4NC B:402BINDING SITE FOR RESIDUE FE B 401
2AC2SOFTWAREHIS B:13 , PRO B:14 , PRO B:15 , HIS B:16 , HIS B:62 , PHE B:86 , TYR B:129 , THR B:192 , HIS B:195 , GLU B:251 , VAL B:279 , ILE B:280 , THR B:282 , FE B:401BINDING SITE FOR RESIDUE 4NC B 402
3AC3SOFTWAREHIS D:13 , HIS D:62 , GLU D:251 , 4NC D:402BINDING SITE FOR RESIDUE FE D 401
4AC4SOFTWAREHIS D:13 , PRO D:15 , HIS D:16 , HIS D:62 , PHE D:86 , TYR D:129 , THR D:192 , HIS D:195 , GLU D:251 , VAL D:279 , ILE D:280 , THR D:282 , FE D:401BINDING SITE FOR RESIDUE 4NC D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VSI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VSI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VSI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VSI)

(-) Exons   (0, 0)

(no "Exon" information available for 3VSI)

(-) Sequences/Alignments

Asymmetric/Biological 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:270
 aligned with AMNA_COMTE | Q6J1Z5 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:270
                                    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
           AMNA_COMTE     2 TVVSAFLVPGTPLPQLKPEVPSWGQLAAATERAGKALAASRPDVVLVYSTQWLAVLDQQWLTRPRSEGVHVDENWYEFGDLAYDIRADTALAEACVTSSPLHGVHARGVNYDGFPIDTGTITACTLMGIGTDAFPLVVGSNNLYHSGEITEKLAALAVDCAKDQNKRVAVVGVGGLSGSLFREEIDPREDRIANEEDDKWNRRVLKLIEAGDVSALREAMPVYAKEARVDMGFKHLHWILGALKGKFSGANVLGYGPSYGSGAAVIEFRL 271
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee...hhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee...eeee...eeeeee....hhhhh.eeeeee.hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeee............hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....eeeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vsi A   2 TVVSAFLVPGTPLPQLKPEVPSWGQLAAATERAGKALAASRPDVVLVYSTQWLAVLDQQWLTRPRSEGVHVDENWYEFGDLAYDIRADTALAEACVTSSPLHGVHARGVNYDGFPIDTGTITACTLMGIGTDAFPLVVGSNNLYHSGEITEKLAALAVDCAKDQNKRVAVVGVGGLSGSLFREEIDPREDRIANEEDDKWNRRVLKLIEAGDVSALREAMPVYAKEARVDMGFKHLHWILGALKGKFSGANVLGYGPSYGSGAAVIEFRL 271
                                    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:304
 aligned with AMNB_COMTE | Q6J1Z6 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:304
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300    
           AMNB_COMTE     1 MQGEIIAGFLAPHPPHLVYGENPPQNEPRSQGGWEVLRWAYERARERLDAMKPDVLLVHSPHWITSVGHHFLGVPELSGKSVDPIFPNVFRYDFSLNVDVELAEACAEEGRKAGLVTKMMRNPKFRVDYGTITTLHLIRPQWDIPVVGISANNSPYYLNTKEGMSEMDVLGKATREAIRKTGRKAVLLASNTLSHWHFHEEPTIPEDMSKEYPATMAGYQWDIRMIELMRQGKTSEVFKLLPQFIDEAFAEVKSGAFTWMHAAMQYPELAAELFGYGTVIGTGNAVMEWDLRKAGLSMLGAADQ 304
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhh.............hhhhhhhhhhhhhhhhh....eeeeeeeeeee...eeee...eeeeeee........eeeeeee.hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh......eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.................hhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeeeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vsi B   1 MQGEIIAGFLAPHPPHLVYGENPPQNEPRSQGGWEVLRWAYERARERLDAMKPDVLLVHSPHWITSVGHHFLGVPELSGKSVDPIFPNVFRYDFSLNVDVELAEACAEEGRKAGLVTKMMRNPKFRVDYGTITTLHLIRPQWDIPVVGISANNSPYYLNTKEGMSEMDVLGKATREAIRKTGRKAVLLASNTLSHWHFHEEPTIPEDMSKEYPATMAGYQWDIRMIELMRQGKTSEVFKLLPQFIDEAFAEVKSGAFTWMHAAMQYPELAAELFGYGTVIGTGNAVMEWDLRKAGLSMLGAADQ 304
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300    


Chain C from PDB  Type:PROTEIN  Length:270
 aligned with AMNA_COMTE | Q6J1Z5 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:270
                                    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
           AMNA_COMTE     2 TVVSAFLVPGTPLPQLKPEVPSWGQLAAATERAGKALAASRPDVVLVYSTQWLAVLDQQWLTRPRSEGVHVDENWYEFGDLAYDIRADTALAEACVTSSPLHGVHARGVNYDGFPIDTGTITACTLMGIGTDAFPLVVGSNNLYHSGEITEKLAALAVDCAKDQNKRVAVVGVGGLSGSLFREEIDPREDRIANEEDDKWNRRVLKLIEAGDVSALREAMPVYAKEARVDMGFKHLHWILGALKGKFSGANVLGYGPSYGSGAAVIEFRL 271
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee...hhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee...eeee...eeeeee..........eeeeee.hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeee............hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....eeeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vsi C   2 TVVSAFLVPGTPLPQLKPEVPSWGQLAAATERAGKALAASRPDVVLVYSTQWLAVLDQQWLTRPRSEGVHVDENWYEFGDLAYDIRADTALAEACVTSSPLHGVHARGVNYDGFPIDTGTITACTLMGIGTDAFPLVVGSNNLYHSGEITEKLAALAVDCAKDQNKRVAVVGVGGLSGSLFREEIDPREDRIANEEDDKWNRRVLKLIEAGDVSALREAMPVYAKEARVDMGFKHLHWILGALKGKFSGANVLGYGPSYGSGAAVIEFRL 271
                                    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:299
 aligned with AMNB_COMTE | Q6J1Z6 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         
           AMNB_COMTE     1 MQGEIIAGFLAPHPPHLVYGENPPQNEPRSQGGWEVLRWAYERARERLDAMKPDVLLVHSPHWITSVGHHFLGVPELSGKSVDPIFPNVFRYDFSLNVDVELAEACAEEGRKAGLVTKMMRNPKFRVDYGTITTLHLIRPQWDIPVVGISANNSPYYLNTKEGMSEMDVLGKATREAIRKTGRKAVLLASNTLSHWHFHEEPTIPEDMSKEYPATMAGYQWDIRMIELMRQGKTSEVFKLLPQFIDEAFAEVKSGAFTWMHAAMQYPELAAELFGYGTVIGTGNAVMEWDLRKAGLSML 299
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhh...........hhhhhhhhhhhhhhhhh....eeeeeeeeeee...eeee...eeeeeee........eeeeeee.hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh......eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.................hhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vsi D   1 MQGEIIAGFLAPHPPHLVYGENPPQNEPRSQGGWEVLRWAYERARERLDAMKPDVLLVHSPHWITSVGHHFLGVPELSGKSVDPIFPNVFRYDFSLNVDVELAEACAEEGRKAGLVTKMMRNPKFRVDYGTITTLHLIRPQWDIPVVGISANNSPYYLNTKEGMSEMDVLGKATREAIRKTGRKAVLLASNTLSHWHFHEEPTIPEDMSKEYPATMAGYQWDIRMIELMRQGKTSEVFKLLPQFIDEAFAEVKSGAFTWMHAAMQYPELAAELFGYGTVIGTGNAVMEWDLRKAGLSML 299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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 3VSI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VSI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VSI)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (AMNA_COMTE | Q6J1Z5)
molecular function
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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.
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:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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.

Chain B,D   (AMNB_COMTE | Q6J1Z6)
molecular function
    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:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
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:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        AMNA_COMTE | Q6J1Z5: 3vsg 3vsh 3vsj
        AMNB_COMTE | Q6J1Z6: 3vsg 3vsh 3vsj

(-) Related Entries Specified in the PDB File

3vsg 3vsh 3vsj