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(-) Description

Title :  THE CRYSTAL STRUCTURE OF 3-HYDROXYANTHRANILATE 3,4-DIOXYGENASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  X. Li, M. Guo, M. Teng, L. Niu
Date :  02 Jun 05  (Deposition) - 02 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Jellyroll Beta-Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Li, M. Guo, M. Teng, L. Niu
The Crystal Structure Of 3-Hydroxyanthranilate 3, 4-Dioxygenase From Saccharomyces Cerevisiae
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-HYDROXYANTHRANILATE 3,4-DIOXYGENASE
    ChainsA, B
    EC Number1.13.11.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Synonym3-HAO, 3- HYDROXYANTHRANILIC ACID DIOXYGENASE, 3- HYDROXYANTHRANILATE OXYGENASE, BIOSYNTHESIS OF NICOTINIC ACID PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NI4Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:49 , GLU A:55 , HIS A:97 , HOH A:205BINDING SITE FOR RESIDUE NI A 201
2AC2SOFTWAREHIS B:49 , GLU B:55 , HIS B:97 , HOH B:205 , HOH B:206BINDING SITE FOR RESIDUE NI B 202
3AC3SOFTWARECYS A:126 , CYS A:129 , CYS A:163 , CYS A:166BINDING SITE FOR RESIDUE NI A 203
4AC4SOFTWARECYS B:126 , CYS B:129 , CYS B:163 , CYS B:166BINDING SITE FOR RESIDUE NI B 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:22 -Pro A:23
2Gly A:41 -Pro A:42
3Pro B:22 -Pro B:23
4Gly B:41 -Pro B:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJR025C1YJR025C.1X:471663-4711305343HAO_YEAST1-1771772A:1-175
B:1-171
175
171

(-) 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:176
 aligned with 3HAO_YEAST | P47096 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:176
                             1                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169      
           3HAO_YEAST     - -MFNTTPINIDKWLKENEGLLKPPVNNYCLHKGGFTVMIVGGPNERTGYHINPTPEWFYQKKGSMLLKVVDETDAEPKFIDIIINEGDSYLLPGNVPHSPVRFADTVGIVVEQDRPGGENDKIRWYCSHCRQVVHESELQMLDLGTQVKEAILDFENDVEKRTCFHCKTLNYARPQ 175
               SCOP domains -d1zvfa1 A:1-175 3-hydroxyanthranilate-3,4-dioxygenase                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eehhhhhhhhhhhhh....eeeee...eeeeee........eee....eeeeeee..eeeeeee......eeeeeee...eeeee.....eeeee....eeeeeee........eeeee......eeeeee......hhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 -Exon 1.1  PDB: A:1-175 UniProt: 1-177 [INCOMPLETE]                                                                                                                              Transcript 1
                 1zvf A   0 AMFNTTPINIDKWLKENEGLLKPPVNNYCLHKGGFTVMIVGGPNERTDYHINPTPEWFYQKKGSMLLKVVDETDAEPKFIDIIINEGDSYLLPGNVPHSPVRFADTVGIVVEQDRPGGENDKIRWYCSHCRQVVHESELQMLDLGTQVKEAILDFENDVEKRTCFHCKTLNYARPQ 175
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169      

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with 3HAO_YEAST | P47096 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:172
                             1                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169  
           3HAO_YEAST     - -MFNTTPINIDKWLKENEGLLKPPVNNYCLHKGGFTVMIVGGPNERTGYHINPTPEWFYQKKGSMLLKVVDETDAEPKFIDIIINEGDSYLLPGNVPHSPVRFADTVGIVVEQDRPGGENDKIRWYCSHCRQVVHESELQMLDLGTQVKEAILDFENDVEKRTCFHCKTLNY 171
               SCOP domains d1zvfb_ B: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -3-HAO-1zvfB01 B:1-155                                                                                                                                      ---------------- Pfam domains (1)
           Pfam domains (2) -3-HAO-1zvfB02 B:1-155                                                                                                                                      ---------------- Pfam domains (2)
         Sec.struct. author .......eehhhhhhhhhhhh.....eeeee...eeeeee........eee....eeeeeee..eeeeeee......eeeeeee...eeeee.....eeeee....eeeeeee........eeeee......eeeeee.......hhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 -Exon 1.1  PDB: B:1-171 UniProt: 1-177 [INCOMPLETE]                                                                                                                          Transcript 1
                 1zvf B   0 AMFNTTPINIDKWLKENEGLLKPPVNNYCLHKGGFTVMIVGGPNERTDYHINPTPEWFYQKKGSMLLKVVDETDAEPKFIDIIINEGDSYLLPGNVPHSPVRFADTVGIVVEQDRPGGENDKIRWYCSHCRQVVHESELQMLDLGTQVKEAILDFENDVEKRTCFHCKTLNY 171
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169  

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (3HAO_YEAST | P47096)
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:0046874    quinolinate metabolic process    The chemical reactions and pathways involving 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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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