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(-) Description

Title :  E2 DNA-BINDING DOMAIN FROM BOVINE PAPILLOMAVIRUS TYPE 1
 
Authors :  R. S. Hegde, A. F. Wang, S. S. Kim, M. Schapira
Date :  05 Jul 01  (Deposition) - 18 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Biol. Unit 3:  C  (2x)
Keywords :  Bpv-1, E2, Dna-Binding Domain, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Hegde, A. F. Wang, S. S. Kim, M. Schapira
Subunit Rearrangement Accompanies Sequence-Specific Dna Binding By The Bovine Papillomavirus-1 E2 Protein.
J. Mol. Biol. V. 276 797 1998
PubMed-ID: 9500927  |  Reference-DOI: 10.1006/JMBI.1997.1587
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN E2
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3D
    Expression System Strain: BD21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN
    Gene: E2
    Organism Scientific: BOVINE PAPILLOMAVIRUS TYPE 1
    Organism Taxid: 10559

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (2x):  B 
Biological Unit 3 (2x):   C

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1JJH)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:340 -C:340

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JJH)

(-) 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:77
 aligned with VE2_BPV1 | P03122 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:86
                                   334       344       354       364       374       384       394       404      
             VE2_BPV1   325 GSCFALISGTANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF 410
               SCOP domains d1jjha_ A: Papillomavirus-1 E2 protein                                                 SCOP domains
               CATH domains 1jjhA00 A:325-410  [code=3.30.70.330, n         o name defined]                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhhh.ee.......---------.eeeeeee.hhhhhhhhhhhh......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 1jjh A 325 ASCFALISGTANQVKCYRFRVKKNHRHRYENCTTTWFTV---------QAQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF 410
                                   334       344       354        |-       374       384       394       404      
                                                                363       373                                     


Chain B from PDB  Type:PROTEIN  Length:78
 aligned with VE2_BPV1 | P03122 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:86
                                   334       344       354       364       374       384       394       404      
             VE2_BPV1   325 GSCFALISGTANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF 410
               SCOP domains d1jjhb_ B: Papillomavirus-1 E2 protein                                                 SCOP domains
               CATH domains 1jjhB00 B:325-410  [code=3.30.70.330, no         name defined]                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhhhhhh.ee........--------.eeeeee..hhhhhhhhhhhh......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 1jjh B 325 ASCFALISGTANQVKCYRFRVKKNHRHRYENCTTTWFTVA--------QAQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF 410
                                   334       344       354       364       374       384       394       404      
                                                                 364      373                                     


Chain C from PDB  Type:PROTEIN  Length:73
 aligned with VE2_BPV1 | P03122 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:85
                                   335       345       355       365       375       385       395       405     
             VE2_BPV1   326 SCFALISGTANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF 410
               SCOP domains d1jjhc_ C: Papillomavirus-1 E2 prote            in                                    SCOP domains
               CATH domains 1jjhC00 C:326-410  [code=3.30.70.330            , no name defined]                    CATH domains
           Pfam domains (1) --PPV_E2_C-1jjhC01 C:328-407                                                      --- Pfam domains (1)
           Pfam domains (2) --PPV_E2_C-1jjhC02 C:328-407                                                      --- Pfam domains (2)
           Pfam domains (3) --PPV_E2_C-1jjhC03 C:328-407                                                      --- Pfam domains (3)
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhhhh.ee.....------------.eeeeee.hhhhhhhhhhhh......eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 1jjh C 326 SCFALISGTANQVKCYRFRVKKNHRHRYENCTTTWF------------AQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF 410
                                   335       345       355     |   -       375       385       395       405     
                                                             361          374
   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: no clan defined [family: PPV_E2_C] (7)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (VE2_BPV1 | P03122)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
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:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0039693    viral DNA genome replication    The replication of a viral DNA genome.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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
        VE2_BPV1 | P03122: 1dbd 2bop 2jeu 2jex

(-) Related Entries Specified in the PDB File

1by9 1BY9 IS E2 DNA-BINDING DOMAIN FROM HUMAN PAPILLOMAVIRUS TYPE 16
1f9f 1F9F IS CRYSTAL STRUCTURE OF THE HPV-18 E2 DNA-BINDING DOMAIN
1jj4 1JJ4 IS HUMAN PAPILLOMAVIRUS TYPE 18 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET
2bop 2BOP IS BOVINE PAPILLOMAVIRUS-E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGE