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(-) Description

Title :  CRYSTAL STRUCTURES OF TWO INTERMEDIATES IN THE ASSEMBLY OF THE PAPILLOMAVIRUS REPLICATION INITIATION COMPLEX
 
Authors :  E. J. Enemark, A. Stenlund, L. Joshua-Tor
Date :  14 Jan 02  (Deposition) - 15 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D,F  (1x)
Biol. Unit 2:  B,E  (2x)
Keywords :  Papillomavirus, Dna-Binding Domain, Replication, Initiator Protein, Helicase, Replication/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Enemark, A. Stenlund, L. Joshua-Tor
Crystal Structures Of Two Intermediates In The Assembly Of The Papillomavirus Replication Initiation Complex.
Embo J. V. 21 1487 2002
PubMed-ID: 11889054  |  Reference-DOI: 10.1093/EMBOJ/21.6.1487
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E1 RECOGNITION SEQUENCE, STRAND 1
    Chains: D, E
    Engineered: YES
    Other Details: 5'-ATAATTGTTGTTAACAATAAT-3'
    Synthetic: YES
 
Molecule 2 - E1 RECOGNITION SEQUENCE, STRAND 2
    Chains: F
    Engineered: YES
    Other Details: 5'-ATTATTGTTAACAACAATTAT-3'
    Synthetic: YES
 
Molecule 3 - REPLICATION PROTEIN E1
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11CGST
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN
    Organism Scientific: BOVINE PAPILLOMAVIRUS
    Organism Taxid: 10571

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD F
Biological Unit 2 (2x):  B  E 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1KSY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KSY)

(-) 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:145
 aligned with VE1_BPV1 | P03116 from UniProtKB/Swiss-Prot  Length:605

    Alignment length:145
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298     
             VE1_BPV1   159 ATVFKLGLFKSLFLCSFHDITRLFKNDKTTNQQWVLAVFGLAEVFFEASFELLKKQCSFLQMQKRSHEGGTCAVYLICFNTAKSRETVRNLMANTLNVREECLMLQPAKIRGLSAALFWFKSSLSPATLKHGALPEWIRAQTTLN 303
               SCOP domains d1ksya_ A: Replication initiation protein E1                                                                                                      SCOP domains
               CATH domains 1ksyA00 A:159-303  [code=3.40.1310.10, no name defined]                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh...........eeeeeee..hhhhhhhhhhhhhhheeeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhh..hhh.eeee.....hhhhhhhhhhhhhh...eeee..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ksy A 159 ATVFKLGLFKSLFLCSFHDITRLFKNDKTTNQQWVLAVFGLAEVFFEASFELLKKQCSFLQMQKRSHEGGTCAVYLICFNTAKSRETVRNLMANMLNVREECLMLQPPKIRGLSAALFWFKSSLSPATLKHGALPEWIRAQTTLN 303
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298     


Chain B from PDB  Type:PROTEIN  Length:148
 aligned with VE1_BPV1 | P03116 from UniProtKB/Swiss-Prot  Length:605

    Alignment length:148
                                   165       175       185       195       205       215       225       235       245       255       265       275       285       295        
             VE1_BPV1   156 SKNATVFKLGLFKSLFLCSFHDITRLFKNDKTTNQQWVLAVFGLAEVFFEASFELLKKQCSFLQMQKRSHEGGTCAVYLICFNTAKSRETVRNLMANTLNVREECLMLQPAKIRGLSAALFWFKSSLSPATLKHGALPEWIRAQTTLN 303
               SCOP domains d1ksyb_ B: Replication initiation protein E1                                                                                                         SCOP domains
               CATH domains 1ksyB00 B:156-303  [code=3.40.1310.10, no name defined]                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhh...........eeeeeee..hhhhhhhhhhhhhhheeeeeeee.......eeeeeeee....hhhhhhhhhhhhh..hhh.eeee.....hhhhhhhhhhhhhh...eeee..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ksy B 156 GSRATVFKLGLFKSLFLCSFHDITRLFKNDKTTNQQWVLAVFGLAEVFFEASFELLKKQCSFLQMQKRSHEGGTCAVYLICFNTAKSRETVRNLMANMLNVREECLMLQPPKIRGLSAALFWFKSSLSPATLKHGALPEWIRAQTTLN 303
                                   165       175       185       195       205       215       225       235       245       255       265       275       285       295        


Chain C from PDB  Type:PROTEIN  Length:145
 aligned with VE1_BPV1 | P03116 from UniProtKB/Swiss-Prot  Length:605

    Alignment length:145
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298     
             VE1_BPV1   159 ATVFKLGLFKSLFLCSFHDITRLFKNDKTTNQQWVLAVFGLAEVFFEASFELLKKQCSFLQMQKRSHEGGTCAVYLICFNTAKSRETVRNLMANTLNVREECLMLQPAKIRGLSAALFWFKSSLSPATLKHGALPEWIRAQTTLN 303
               SCOP domains d1ksyc_ C: Replication initiation protein E1                                                                                                      SCOP domains
               CATH domains 1ksyC00 C:159-303  [code=3.40.1310.10, no name defined]                                                                                           CATH domains
           Pfam domains (1) -------PPV_E1_C-1ksyC01 C:166-303                                                                                                                 Pfam domains (1)
           Pfam domains (2) -------PPV_E1_C-1ksyC02 C:166-303                                                                                                                 Pfam domains (2)
           Pfam domains (3) -------PPV_E1_C-1ksyC03 C:166-303                                                                                                                 Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh...........eeeeeee..hhhhhhhhhhhhhhheeeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhh..hhh.eeee.....hhhhhhhhhhhhhh...eeee..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ksy C 159 ATVFKLGLFKSLFLCSFHDITRLFKNDKTTNQQWVLAVFGLAEVFFEASFELLKKQCSFLQMQKRSHEGGTCAVYLICFNTAKSRETVRNLMANMLNVREECLMLQPPKIRGLSAALFWFKSSLSPATLKHGALPEWIRAQTTLN 303
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298     


Chain D from PDB  Type:DNA  Length:21
                                                     
                 1ksy D   1 ATAATTGTTGTCAACAATTAT  21
                                    10        20 


Chain E from PDB  Type:DNA  Length:21
                                                     
                 1ksy E   1 ATAATTGTTGTCAACAATTAT  21
                                    10        20 


Chain F from PDB  Type:DNA  Length:21
                                                     
                 1ksy F   1 ATAATTGTTGACAACAATTAT  21
                                    10        20
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (VE1_BPV1 | P03116)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004003    ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    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: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).
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.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VE1_BPV1 | P03116: 1f08 1ksx 2gxa 2v9p 5a9k

(-) Related Entries Specified in the PDB File

1f08 BPV E1 DNA-BINDING DOMAIN NOT BOUND TO DNA
1ksx CRYSTAL STRUCTURES OF TWO INTERMEDIATES IN THE ASSEMBLY OF THE PAPILLOMAVIRUS REPLICATION INITIATION COMPLEX