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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX OF PTERIN-4A-CARBINOLAMINE DEHYDRATASE FROM TOXOPLASMA GONDII WITH 7,8-DIHYDROBIOPTERIN
 
Authors :  S. Cameron, S. A. Fyffe, W. N. Hunter
Date :  20 Jul 07  (Deposition) - 22 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lyase, Pterin, Enzyme, Tautomer, Toxoplasma, Dehydratase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Cameron, S. A. Fyffe, S. Goldie, W. N. Hunter
Crystal Structures Of Toxoplasma Gondii Pterin-4A- Carbinolamine Dehydratase And Comparisons With Mammalian And Parasite Orthologues.
Mol. Biochem. Parasitol. V. 158 131 2008
PubMed-ID: 18215430  |  Reference-DOI: 10.1016/J.MOLBIOPARA.2007.12.002

(-) Compounds

Molecule 1 - PTERIN-4A-CARBINOLAMINE DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.96
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET15B (NOVAGEN)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: TOXOPLASMA GONDII
    Organism Taxid: 383379
    Strain: RH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1H2B2Ligand/Ion2-AMINO-6-(1,2-DIHYDROXY-PROPYL)-7,8-DIHYDRO-6H-PTERIDIN-4-ONE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1H2B4Ligand/Ion2-AMINO-6-(1,2-DIHYDROXY-PROPYL)-7,8-DIHYDRO-6H-PTERIDIN-4-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:60 , HIS A:61 , HIS A:62 , SER A:77 , HIS A:79 , ASP A:80 , TYR B:69BINDING SITE FOR RESIDUE H2B A1104
2AC2SOFTWAREASP B:60 , HIS B:61 , HIS B:62 , HIS B:79 , ASP B:80BINDING SITE FOR RESIDUE H2B B1104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V6T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V6T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V6T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V6T)

(-) Exons   (0, 0)

(no "Exon" information available for 2V6T)

(-) 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:99
 aligned with Q2Q449_TOXGO | Q2Q449 from UniProtKB/TrEMBL  Length:104

    Alignment length:99
                                    14        24        34        44        54        64        74        84        94         
         Q2Q449_TOXGO     5 ARLAANSARLLQLHKTVPQWHLTDGHLSIKRKFQFSDFNEAWGFMSRVALYADKVDHHPNWYNVYNTVDVELSTHDAAGLTEKDFALAKFMDDAAKNFE 103
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2v6tA00 A:5-103  [code=3.30.1360.20, no name defined]                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh...eeee.....eeeeee...hhhhhhhhhhhhhhhhhh....eeeee..eeeeee.........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 2v6t A   5 ARLAANSARLLQLHKTVPQWHLTDGHLSIKRKFQFSDFNEAWGFMSRVALYADKVDHHPNWYNVYNTVDVELSTHDAAGLTEKDFALAKFMDDAAKNFE 103
                                    14        24        34        44        54        64        74        84        94         


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with Q2Q449_TOXGO | Q2Q449 from UniProtKB/TrEMBL  Length:104

    Alignment length:100
                                    13        23        33        43        53        63        73        83        93       103
         Q2Q449_TOXGO     4 LARLAANSARLLQLHKTVPQWHLTDGHLSIKRKFQFSDFNEAWGFMSRVALYADKVDHHPNWYNVYNTVDVELSTHDAAGLTEKDFALAKFMDDAAKNFE 103
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2v6tB00 B:4-103  [code=3.30.1360.20, no name defined]                                                CATH domains
           Pfam domains (1) -Pterin_4a-2v6tB01 B:5-100                                                                       --- Pfam domains (1)
           Pfam domains (2) -Pterin_4a-2v6tB02 B:5-100                                                                       --- Pfam domains (2)
         Sec.struct. author ........hhhhhhhhh...eeee.....eeeeee...hhhhhhhhhhhhhhhhhh....eeeee..eeeeee........................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2v6t B   4 LARLAANSARLLQLHKTVPQWHLTDGHLSIKRKFQFSDFNEAWGFMSRVALYADKVDHHPNWYNVYNTVDVELSTHDAAGLTEKDFALAKFMDDAAKNFE 103
                                    13        23        33        43        53        63        73        83        93       103
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2V6T)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Pterin_4a] (7)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q2Q449_TOXGO | Q2Q449)
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.
biological process
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q2Q449_TOXGO | Q2Q449: 2v6s 2v6u

(-) Related Entries Specified in the PDB File

2v6s MEDIUM RESOLUTION CRYSTAL STRUCTURE OF PETRIN -4A-CARBINOLAMINE DEHYDRATASE FROM TOXOPLASMA GONDII
2v6u HIGH RESOLUTION CRYSTAL STRUCTURE OF PTERIN- 4A-CARBINOLAMINE DEHYDRATASE FROM TOXOPLASMA GONDII