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(-) Description

Title :  STRUCTURE OF THE ZINC-BINDING DOMAIN OF BACILLUS STEAROTHERMOPHILUS DNA PRIMASE
 
Authors :  H. Pan, D. B. Wigley
Date :  14 Sep 99  (Deposition) - 29 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Primase, Zinc-Binding Motif, Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Pan, D. B. Wigley
Structure Of The Zinc-Binding Domain Of Bacillus Stearothermophilus Dna Primase.
Structure Fold. Des. V. 8 231 2000
PubMed-ID: 10745010  |  Reference-DOI: 10.1016/S0969-2126(00)00101-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA PRIMASE
    ChainsA, B
    EC Number2.7.7.-
    EngineeredYES
    Expression SystemGEOBACILLUS STEAROTHERMOPHILUS
    Expression System PlasmidPET21D
    Expression System Taxid1422
    Expression System Vector TypePLASMID
    FragmentZINC-BINDING DOMAIN
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:40 , HIS A:43 , CYS A:61 , CYS A:64BINDING SITE FOR RESIDUE ZN A 151
2AC2SOFTWARECYS B:40 , HIS B:43 , CYS B:61 , CYS B:64BINDING SITE FOR RESIDUE ZN B 151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D0Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D0Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D0Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D0Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1D0Q)

(-) 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:102
 aligned with DNAG_GEOSE | Q9X4D0 from UniProtKB/Swiss-Prot  Length:597

    Alignment length:102
                                    11        21        31        41        51        61        71        81        91       101  
           DNAG_GEOSE     2 GHRIPEETIEAIRRGVDIVDVIGEYVQLKRQGRNYFGLCPFHGEKTPSFSVSPEKQIFHCFGCGAGGNAFTFLMDIEGIPFVEAAKRLAAKAGVDLSVYELD 103
               SCOP domains d1d0qa_ A: Zinc-binding domain of DNA primase                                                          SCOP domains
               CATH domains 1d0qA00 A:2-103 DNA Primase; Chain A                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.....eee..eeee...........eeee....eeee.....eehhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1d0q A   2 GHRIPEETIEAIRRGVDIVDVIGEYVQLKRQGRNYFGLCPFHGEKTPSFSVSPEKQIFHCFGCGAGGNAFTFLMDIEGIPFVEAAKRLAAKAGVDLSVYELD 103
                                    11        21        31        41        51        61        71        81        91       101  

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with DNAG_GEOSE | Q9X4D0 from UniProtKB/Swiss-Prot  Length:597

    Alignment length:102
                                    11        21        31        41        51        61        71        81        91       101  
           DNAG_GEOSE     2 GHRIPEETIEAIRRGVDIVDVIGEYVQLKRQGRNYFGLCPFHGEKTPSFSVSPEKQIFHCFGCGAGGNAFTFLMDIEGIPFVEAAKRLAAKAGVDLSVYELD 103
               SCOP domains d1d0qb_ B: Zinc-binding domain of DNA primase                                                          SCOP domains
               CATH domains 1d0qB00 B:2-103 DNA Primase; Chain A                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.hhhhhhhh....eee..eeee...........eeee....eeee.....eehhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1d0q B   2 GHRIPEETIEAIRRGVDIVDVIGEYVQLKRQGRNYFGLCPFHGEKTPSFSVSPEKQIFHCFGCGAGGNAFTFLMDIEGIPFVEAAKRLAAKAGVDLSVYELD 103
                                    11        21        31        41        51        61        71        81        91       101  

   Legend:   → Mismatch (orange background)
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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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D0Q)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DNAG_GEOSE | Q9X4D0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0003896    DNA primase activity    Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases.
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006269    DNA replication, synthesis of RNA primer    The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.
cellular component
    GO:1990077    primosome complex    Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart.

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 Related Entries

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        DNAG_GEOSE | Q9X4D01z8s 2r6a 2r6c 4m4w

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