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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE 2 (PCBD2)
 
Authors :  J. Kopec, W. Kiyani, M. Vollmar, L. Shrestha, P. Canning, F. Von Delft, N. Burgess-Brown, C. Bountra, C. H. Arrowsmith, A. Edwards, W. W. Yue
Date :  30 Aug 13  (Deposition) - 11 Sep 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Kopec, W. Kiyani, M. Vollmar, L. Shrestha, P. Canning, F. Von Delft N. Burgess-Brown, C. Bountra, C. H. Arrowsmith, A. Edwards, W. W. Yue
Crystal Structure Of Human Pterin-4-Alpha- Carbinolamine Dehydratase 2 (Pcbd2)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE 2
    ChainsA
    EC Number4.2.1.96
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28BSA
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA
    Expression System Vector TypePLASMID
    FragmentRESIDUES 28-130
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHS 2,4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE 2, DCOH -LIKE PROTEIN DCOHM, DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1 FROM MUSCLE, HNF-1-ALPHA DIMERIZATION COFACTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:39 , SER A:40 , HOH A:2052 , HOH A:2055 , HOH A:2099BINDING SITE FOR RESIDUE EDO A1105

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C45)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C45)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C45)

(-) Exons   (0, 0)

(no "Exon" information available for 4C45)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:99
 aligned with PHS2_HUMAN | Q9H0N5 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:99
                                    41        51        61        71        81        91       101       111       121         
           PHS2_HUMAN    32 THRLTAEERNQAILDLKAAGWSELSERDAIYKEFSFHNFNQAFGFMSRVALQAEKMNHHPEWFNVYNKVQITLTSHDCGELTKKDVKLAKFIEKAAASV 130
               SCOP domains d4c45a_ A: automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..ee......eeeeee..hhhhhhhhhhhhhhhhhhhh...eeeee..eeeeee........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4c45 A   6 THRLTAEERNQAILDLKAAGWSELSERDAIYKEFSFHNFNQAFGFMSRVALQAEKMNHHPEWFNVYNKVQITLTSHDCGELTKKDVKLAKFIEKAAASV 104
                                    15        25        35        45        55        65        75        85        95         

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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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C45)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C45)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (PHS2_HUMAN | Q9H0N5)
molecular function
    GO:0008124    4-alpha-hydroxytetrahydrobiopterin dehydratase activity    Catalysis of the reaction: (6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7,8-tetrahydro-4a-hydroxypterin = (6R)-6-(L-erythro-1,2-dihydroxypropyl)-7,8-dihydro-6H-pterin + H(2)O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004505    phenylalanine 4-monooxygenase activity    Catalysis of the reaction: L-phenylalanine + tetrahydrobiopterin + O2 = L-tyrosine + 4-alpha-hydroxytetrahydrobiopterin.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051291    protein heterooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0006729    tetrahydrobiopterin biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrobiopterin, the reduced form of biopterin (2-amino-4-hydroxy-6-(1,2-dihydroxypropyl)-pteridine). It functions as a hydroxylation coenzyme, e.g. in the conversion of phenylalanine to tyrosine.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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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