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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHAGE P4 ORIGIN-BINDING DOMAIN
 
Authors :  H. J. Yeo, G. Ziegelin, S. Korolev, R. Calendar, E. Lanka, G. Waksman
Date :  31 Oct 01  (Deposition) - 17 Apr 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Winged Helix, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Yeo, G. Ziegelin, S. Korolev, R. Calendar, E. Lanka, G. Waksman
Phage P4 Origin-Binding Domain Structure Reveals A Mechanism For Regulation Of Dna-Binding Activity By Homo- And Heterodimerization Of Winged Helix Proteins.
Mol. Microbiol. V. 43 855 2002
PubMed-ID: 11929537  |  Reference-DOI: 10.1046/J.1365-2958.2002.02796.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE P4-SPECIFIC DNA PRIMASE
    Chains: A, B, C, D, E, F
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: ORIGIN-BINDING DOMAIN
    Organism Scientific: ENTEROBACTERIA PHAGE P4
    Organism Taxid: 10680

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1KA8)

(-) Sites  (0, 0)

(no "Site" information available for 1KA8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KA8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KA8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KA8)

(-) Exons   (0, 0)

(no "Exon" information available for 1KA8)

(-) 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:100
 aligned with PRIM_BPP4 | P10277 from UniProtKB/Swiss-Prot  Length:777

    Alignment length:100
                                   680       690       700       710       720       730       740       750       760       770
            PRIM_BPP4   671 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 770
               SCOP domains d1ka8a_ A: P4 origin-binding domain                                                                  SCOP domains
               CATH domains 1ka8A00 A:1-100 'winged helix' repressor DNA binding domain                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..eee.....................hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.....eeee..eeee.eee.hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1ka8 A   1 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 100
                                    10        20        30        40        50        60        70        80        90       100


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with PRIM_BPP4 | P10277 from UniProtKB/Swiss-Prot  Length:777

    Alignment length:100
                                   680       690       700       710       720       730       740       750       760       770
            PRIM_BPP4   671 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 770
               SCOP domains d1ka8b_ B: P4 origin-binding domain                                                                  SCOP domains
               CATH domains 1ka8B00 B:1-100 'winged helix' repressor DNA binding domain                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.eee.....................hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.....eeee..eeee.eee.hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1ka8 B   1 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 100
                                    10        20        30        40        50        60        70        80        90       100


Chain C from PDB  Type:PROTEIN  Length:100
 aligned with PRIM_BPP4 | P10277 from UniProtKB/Swiss-Prot  Length:777

    Alignment length:100
                                   680       690       700       710       720       730       740       750       760       770
            PRIM_BPP4   671 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 770
               SCOP domains d1ka8c_ C: P4 origin-binding domain                                                                  SCOP domains
               CATH domains 1ka8C00 C:1-100 'winged helix' repressor DNA binding domain                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..eee.....................hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.....eeee..eeee.eeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1ka8 C   1 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 100
                                    10        20        30        40        50        60        70        80        90       100


Chain D from PDB  Type:PROTEIN  Length:100
 aligned with PRIM_BPP4 | P10277 from UniProtKB/Swiss-Prot  Length:777

    Alignment length:100
                                   680       690       700       710       720       730       740       750       760       770
            PRIM_BPP4   671 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 770
               SCOP domains d1ka8d_ D: P4 origin-binding domain                                                                  SCOP domains
               CATH domains 1ka8D00 D:1-100 'winged helix' repressor DNA binding domain                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..eee.....................hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.....eee....eee.eeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1ka8 D   1 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 100
                                    10        20        30        40        50        60        70        80        90       100


Chain E from PDB  Type:PROTEIN  Length:100
 aligned with PRIM_BPP4 | P10277 from UniProtKB/Swiss-Prot  Length:777

    Alignment length:100
                                   680       690       700       710       720       730       740       750       760       770
            PRIM_BPP4   671 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 770
               SCOP domains d1ka8e_ E: P4 origin-binding domain                                                                  SCOP domains
               CATH domains 1ka8E00 E:1-100 'winged helix' repressor DNA binding domain                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..eee.....................hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh................eeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1ka8 E   1 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 100
                                    10        20        30        40        50        60        70        80        90       100


Chain F from PDB  Type:PROTEIN  Length:100
 aligned with PRIM_BPP4 | P10277 from UniProtKB/Swiss-Prot  Length:777

    Alignment length:100
                                   680       690       700       710       720       730       740       750       760       770
            PRIM_BPP4   671 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 770
               SCOP domains d1ka8f_ F: P4 origin-binding domain                                                                  SCOP domains
               CATH domains 1ka8F00 F:1-100 'winged helix' repressor DNA binding domain                                          CATH domains
           Pfam domains (1) Pox_D5-1ka8F01 F:1-99                                                                              - Pfam domains (1)
           Pfam domains (2) Pox_D5-1ka8F02 F:1-99                                                                              - Pfam domains (2)
           Pfam domains (3) Pox_D5-1ka8F03 F:1-99                                                                              - Pfam domains (3)
           Pfam domains (4) Pox_D5-1ka8F04 F:1-99                                                                              - Pfam domains (4)
           Pfam domains (5) Pox_D5-1ka8F05 F:1-99                                                                              - Pfam domains (5)
           Pfam domains (6) Pox_D5-1ka8F06 F:1-99                                                                              - Pfam domains (6)
         Sec.struct. author ..hhhhhhh..eee.....................hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh................eeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1ka8 F   1 DADPTFDFIGYLETLPQTSGMYMGNASIIPRNYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKEYGLNYEKRHTKQGIQTNLTLKEESYGDWLPK 100
                                    10        20        30        40        50        60        70        80        90       100
   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  (1, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (PRIM_BPP4 | P10277)
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: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:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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: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.

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  1ka8
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