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(-) Description

Title :  THE STRUCTURE OF PHAGE PHI29 REPLICATION ORGANIZER PROTEIN P16.7 IN COMPLEX WITH DOUBLE STRANDED DNA
 
Authors :  A. Albert, M. Jimenez, D. Munoz-Espin, J. L. Asensio, J. A. Hermoso, M. S W. J. J. Meijer
Date :  31 Oct 05  (Deposition) - 08 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,Y,Z
Keywords :  Dna-Binding Protein-Dna Complex, Dna-Binding Protein, Complex (Dna-Binding Protein/Dna) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Albert, D. Munoz-Espin, M. Jimenez, J. L. Asensio, J. A. Hermoso, M. Salas, W. J. J. Meijer
Structural Basis For Membrane Anchorage Of Viral Phi 29 Dna During Replication.
J. Biol. Chem. V. 280 42486 2005
PubMed-ID: 16275651  |  Reference-DOI: 10.1074/JBC.C500429200

(-) Compounds

Molecule 1 - EARLY PROTEIN P16.7
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 64-130
    Organism ScientificBACILLUS PHAGE PHI29
    Organism Taxid10756
    Other DetailsDSDNA AND SSDNA BINDING PROTEIN
 
Molecule 2 - 5'-D(*TP*CP*CP*AP*CP*CP*GP*GP)-3'
    ChainsY
    SyntheticYES
 
Molecule 3 - 5'-D(*CP*CP*GP*GP*TP*GP*GP*AP)-3'
    ChainsZ
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit ABCDEFYZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2C5R)

(-) Sites  (0, 0)

(no "Site" information available for 2C5R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C5R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C5R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C5R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C5R)

(-) Exons   (0, 0)

(no "Exon" information available for 2C5R)

(-) 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:64
 aligned with GP167_BPPH2 | P16517 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:64
                                    76        86        96       106       116       126    
          GP167_BPPH2    67 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 130
               SCOP domains d2c5ra1 A:66-129 Early protein gp16.7                            SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2c5r A  66 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 129
                                    75        85        95       105       115       125    

Chain B from PDB  Type:PROTEIN  Length:64
 aligned with GP167_BPPH2 | P16517 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:64
                                    76        86        96       106       116       126    
          GP167_BPPH2    67 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 130
               SCOP domains d2c5rb_ B: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2c5r B  66 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 129
                                    75        85        95       105       115       125    

Chain C from PDB  Type:PROTEIN  Length:64
 aligned with GP167_BPPH2 | P16517 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:64
                                    76        86        96       106       116       126    
          GP167_BPPH2    67 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 130
               SCOP domains d2c5rc_ C: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2c5r C  66 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 129
                                    75        85        95       105       115       125    

Chain D from PDB  Type:PROTEIN  Length:64
 aligned with GP167_BPPH2 | P16517 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:64
                                    76        86        96       106       116       126    
          GP167_BPPH2    67 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 130
               SCOP domains d2c5rd_ D: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2c5r D  66 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 129
                                    75        85        95       105       115       125    

Chain E from PDB  Type:PROTEIN  Length:64
 aligned with GP167_BPPH2 | P16517 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:64
                                    76        86        96       106       116       126    
          GP167_BPPH2    67 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 130
               SCOP domains d2c5re_ E: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2c5r E  66 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 129
                                    75        85        95       105       115       125    

Chain F from PDB  Type:PROTEIN  Length:64
 aligned with GP167_BPPH2 | P16517 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:64
                                    76        86        96       106       116       126    
          GP167_BPPH2    67 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 130
               SCOP domains d2c5rf_ F: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2c5r F  66 NLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK 129
                                    75        85        95       105       115       125    

Chain Y from PDB  Type:DNA  Length:8
                                        
                 2c5r Y   9 TCCACCGG  16

Chain Z from PDB  Type:DNA  Length:8
                                        
                 2c5r Z   1 CCGGTGGA   8

   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, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C5R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C5R)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (GP167_BPPH2 | P16517)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    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:0039693    viral DNA genome replication    The replication of a viral DNA genome.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GP167_BPPH2 | P165171zae 2bnk

(-) Related Entries Specified in the PDB File

1zae SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PHI29 REPLICATION ORGANIZER P16.7C
2bnk THE STRUCTURE OF PHAGE PHI29 REPLICATION ORGANIZER PROTEIN P16.7