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(-) Description

Title :  CRYSTAL STRUCTURE OF THE E2 DNA-BINDING DOMAIN FROM HUMAN PAPILLOMAVIRUS TYPE-16: IMPLICATIONS FOR ITS DNA BINDING-SITE SELECTION MECHANISM
 
Authors :  R. S. Hegde, E. J. Androphy
Date :  27 Oct 98  (Deposition) - 27 Apr 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Papillomavirus, Transcription Regulation, Beta-Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Hegde, E. J. Androphy
Crystal Structure Of The E2 Dna-Binding Domain From Human Papillomavirus Type 16: Implications For Its Dna Binding-Site Selection Mechanism.
J. Mol. Biol. V. 284 1479 1998
PubMed-ID: 9878365  |  Reference-DOI: 10.1006/JMBI.1998.2260
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN E2
    Cell Line: BL21
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BL21
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: DNA-BINDING DOMAIN
    Gene: E2
    Organism Scientific: HUMAN PAPILLOMAVIRUS TYPE 16
    Organism Taxid: 333760

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:72
 aligned with VE2_HPV16 | P03120 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:80
                                   294       304       314       324       334       344       354       364
            VE2_HPV16   285 TTPIVHLKGDANTLKCLRYRFKKHCTLYTAVSSTWHWTGHNVKHKSAIVTLTYDSEWQRDQFLSQVKIPKTITVSTGFMS 364
               SCOP domains d1by9a_ A: Papillomavirus-1 E2 protein                                           SCOP domains
               CATH domains 1by9A00 A:283-362  [code=3.30.70.330,         no name defined]                   CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhhhhhhhhhhhhh...........--------eeeeee...hhhhhhhhhh.......eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 1by9 A 283 TTPIVHLKGDANTLKCLRYRFKKHCTLYTAVSSTWHWT--------AIVTLTYDSEWQRDQFLSQVKIPKTITVSTGFMS 362
                                   292       302       312       | -      |332       342       352       362
                                                               320      329
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BY9)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (VE2_HPV16 | P03120)
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: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.
    GO:0044163    host cytoskeleton    Any of the various filamentous elements that form the internal framework of host cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the host cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the host cell. The various elements of the host cytoskeleton not only serve in the maintenance of host cellular shape but also have roles in other host cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

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 Related Entries

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        VE2_HPV16 | P03120: 1dto 1r8p 1zzf 2nnu 2q79 3mi7

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