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(-) Description

Title :  CRYSTAL STRUCTURE OF A 6-PYRUVOYLTETRAHYDROPTERIN SYNTHASE HOMOLOGUE FROM ESHERICHIA COLI
 
Authors :  K. H. Seo, N. N. Zhuang, K. H. Lee
Date :  08 Feb 11  (Deposition) - 07 Dec 11  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  A,B  (1x)
Keywords :  6-Pyruvoyltetrahydropterin Synthase, Bh4 Synthase, Zn, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Seo, N. Zhuang, Y. S. Park, K. H. Park, K. H. Lee
Structural Basis Of A Novel Activity Of Bacterial 6-Pyruvoyltetrahydropterin Synthase Homologues Distinct Fro Mammalian 6-Pyruvoyltetrahydropterin Synthase Activity.
Acta Crystallogr. , Sect. D V. 70 1212 2014
PubMed-ID: 24816091  |  Reference-DOI: 10.1107/S1399004714002016

(-) Compounds

Molecule 1 - 6-PYRUVOYL TETRAHYDROBIOPTERIN SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ECDH1_0923
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 469008
    Strain: BL21(DE3)
    Synonym: 6-PYRUVOYLTETRAHYDROPTERIN SYNTHASE, PTPS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:16 , HIS A:31 , HIS A:33BINDING SITE FOR RESIDUE ZN A 122
2AC2SOFTWAREHIS B:16 , HIS B:31 , HIS B:33 , GLU B:110BINDING SITE FOR RESIDUE ZN B 122

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QN9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QN9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QN9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QN9)

(-) Exons   (0, 0)

(no "Exon" information available for 3QN9)

(-) 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:118
 aligned with QUED_ECOLI | P65870 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
           QUED_ECOLI     2 MSTTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYR 119
               SCOP domains d3qn9a_ A: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee........hhhhh.eeeeeeeeeeee............hhhhhhhhhhhhhhhh.ee.hhh......hhhhhhhhhhhhhhhhh..eeeeeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3qn9 A   2 MSTTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYR 119
                                    11        21        31        41        51        61        71        81        91       101       111        


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with QUED_ECOLI | P65870 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:117
                                    13        23        33        43        53        63        73        83        93       103       113       
           QUED_ECOLI     4 TTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
               SCOP domains d3qn9b_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..............eeeeeeeeeeee............hhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhhh..eeeeeee......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3qn9 B   4 TTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
                                    13        23        33        43        53        63        73        83        93       103       113
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QN9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QN9)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (QUED_ECOLI | P65870)
molecular function
    GO:0070497    6-carboxy-5,6,7,8-tetrahydropterin synthase activity    Catalysis of the reaction: 7,8-dihydroneopterin triphosphate + H2O = 6-carboxy-5,6,7,8-tetrahydropterin + triphosphate + acetaldehyde + 2 H+.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008616    queuosine biosynthetic process    The chemical reactions and pathways resulting in the formation of queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents.

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  4.2.3.12
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 Related Entries

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

UniProtKB/Swiss-Prot
        QUED_ECOLI | P65870: 3qn0 3qna 4ntk 4ntm 4ntn

(-) Related Entries Specified in the PDB File

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