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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-HYDROXYANTHRANILATE-3,4-DIOXYGENASE FROM RALSTONIA METALLIDURANS COMPLEXED WITH 4-CHLORO-3-HYDROXYANTHRANILIC ACID AND NO
 
Authors :  Y. Zhang, K. L. Colabroy, T. P. Begley, S. E. Ealick
Date :  04 Jan 05  (Deposition) - 31 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cupin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, K. L. Colabroy, T. P. Begley, S. E. Ealick
Structural Studies On 3-Hydroxyanthranilate-3, 4-Dioxygenase The Catalytic Mechanism Of A Complex Oxidation Involved In Nad Biosynthesis.
Biochemistry V. 44 7632 2005
PubMed-ID: 15909978  |  Reference-DOI: 10.1021/BI047353L

(-) Compounds

Molecule 1 - 3-HYDROXYANTHRANILATE-3,4-DIOXYGENASE
    Chains: A
    EC Number: 1.13.11.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: CUPRIAVIDUS METALLIDURANS
    Organism Taxid: 119219

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
14AA1Ligand/Ion4-CHLORO-3-HYDROXYANTHRANILIC ACID
2FE2Ligand/IonFE (III) ION
3NO1Ligand/IonNITRIC OXIDE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
14AA2Ligand/Ion4-CHLORO-3-HYDROXYANTHRANILIC ACID
2FE-1Ligand/IonFE (III) ION
3NO-1Ligand/IonNITRIC OXIDE
4TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:51 , GLU A:57 , HIS A:95 , NO A:310 , 4AA A:401BINDING SITE FOR RESIDUE FE A 300
2AC2SOFTWARECYS A:125 , CYS A:128 , CYS A:162 , CYS A:165BINDING SITE FOR RESIDUE FE A 301
3AC3SOFTWAREARG A:47 , HIS A:51 , HIS A:95 , PRO A:97 , FE A:300 , 4AA A:401BINDING SITE FOR RESIDUE NO A 310
4AC4SOFTWAREVAL A:132 , HIS A:133 , ASP A:158 , LYS A:159 , ARG A:161 , PRO A:163 , HOH A:432 , HOH A:439BINDING SITE FOR RESIDUE TRS A 400
5AC5SOFTWAREVAL A:41 , ARG A:47 , HIS A:51 , GLU A:57 , PHE A:59 , PRO A:97 , ARG A:99 , GLU A:110 , ILE A:142 , FE A:300 , NO A:310 , HOH A:418BINDING SITE FOR RESIDUE 4AA A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:23 -Pro A:24
2Gly A:43 -Pro A:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YFX)

(-) 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:174
 aligned with 3HAO_CUPMC | Q1LCS4 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
           3HAO_CUPMC     1 MLTYGAPFNFPRWIDEHAHLLKPPVGNRQVWQDSDFIVTVVGGPNHRTDYHDDPLEEFFYQLRGNAYLNLWVDGRRERADLKEGDIFLLPPHVRHSPQRPEAGSACLVIERQRPAGMLDGFEWYCDACGHLVHRVEVQLKSIVTDLPPLFESFYASEDKRRCPHCGQVHPGRAA 174
               SCOP domains d1yfxa_ A: 3-hydroxyanthranilate-3,4-dioxygenase                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh.....eee......eeeeee........eee....eeeeeee..eeeeee....eeeeee....eeee.....eeee......eeeeeee.......eeeeee......eeeeeee.......hhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yfx A   1 MLTYGAPFNFPRWIDEHAHLLKPPVGNRQVWQDSDFIVTVVGGPNHRTDYHDDPLEEFFYQLRGNAYLNLWVDGRRERADLKEGDIFLLPPHVRHSPQRPEAGSACLVIERQRPAGMLDGFEWYCDACGHLVHRVEVQLKSIVTDLPPLFESFYASEDKRRCPHCGQVHPGRAA 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YFX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (3HAO_CUPMC | Q1LCS4)
molecular function
    GO:0000334    3-hydroxyanthranilate 3,4-dioxygenase activity    Catalysis of the reaction: 3-hydroxyanthranilate + O(2) = cis,cis-2-amino-3-(3-oxoprop-1-enyl)but-2-enedioate + H(+).
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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:0034354    'de novo' NAD biosynthetic process from tryptophan    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of tryptophan from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0009435    NAD biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0043420    anthranilate metabolic process    The chemical reactions and pathways involving anthranilate (2-aminobenzoate).
    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.
    GO:0019363    pyridine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.
    GO:0019805    quinolinate biosynthetic process    The chemical reactions and pathways resulting in the formation of quinolinate, the anion of quinolinic acid, also known as 2,3-pyridinedicarboxylic acid.
    GO:0006569    tryptophan catabolic process    The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        3HAO_CUPMC | Q1LCS4: 1yfu 1yfw 1yfy 4hsj 4hsl 4hvo 4hvq 4hvr 4i3p 4l2n 4r52 4wzc

(-) Related Entries Specified in the PDB File

1yfu THE UNLIGANDED STRUCTURE
1yfw
1yfy