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(-) Description

Title :  N512P MUTANT OF THE DNA BINDING DOMAIN OF THE ADENOVIRUS 5 SSDNA BINDING PROTEIN
 
Authors :  J. Hendle, P. N. Kanellopoulos, P. A. Tucker
Date :  19 Feb 09  (Deposition) - 31 Mar 10  (Release) - 31 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  X
Keywords :  Dna-Binding Protein, Ssdna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hendle, P. N. Kanellopoulos, P. A. Tucker
High Resolution Structures Of The Adenovirus Single-Stranded Dna Binding Protein And The N512P Hinge-Region Mutant
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - E2A DNA-BINDING PROTEIN
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: C-TERMINAL DNA BINDING DOMAIN, RESIDUES 174-529
    Mutation: YES
    Organism Scientific: HUMAN ADENOVIRUS 5
    Organism Taxid: 28285
    Synonym: ADENOVIRUS 5 SSDNA BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS X:284 , HIS X:286 , CYS X:339 , CYS X:355BINDING SITE FOR RESIDUE ZN X 601
2AC2SOFTWARECYS X:396 , CYS X:398 , CYS X:450 , CYS X:467BINDING SITE FOR RESIDUE ZN X 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WAZ)

(-) 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 X from PDB  Type:PROTEIN  Length:315
 aligned with DNB2_ADE05 | P03265 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:354
                                   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525    
           DNB2_ADE05   176 PIVSAWEKGMEAARALMDKYHVDNDLKANFKLLPDQVEALAAVCKTWLNEEHRGLQLTFTSKKTFVTMMGRFLQAYLQSFAEVTYKHHEPTGCALWLHRCAEIEGELKCLHGSIMINKEHVIEMDVTSENGQRALKEQSSKAKIVKNRWGRNVVQISNTDARCCVHDAACPANQFSGKSCGMFFSEGAKAQVAFKQIKAFMQALYPNAQTGHGHLLMPLRCECNSKPGHAPFLGRQLPKLTPFALSNAEDLDADLISDKSVLASVHHPALIVFQCCNPVYRNSRAQGGGPNCDFKISAPDLLNALVMVRSLWSENFTELPRMVVPEFKWSTKHQYRNVSLPVAHSDARQNPFDF 529
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2wazX01 X:176-266,X:474-500 Adenovirus Single-stranded Dna-binding Protein, domain 1       2wazX02 X:267-473 Adenovirus Sin                               gle-stranded Dna-binding Protein, domain 2                                                                                                      2wazX01 X:176-266,X:474-500----------------------------- CATH domains
           Pfam domains (1) Viral_DNA_bi-2wazX03 X:176-264                                                           ----------------------------------                               ----------------------------------------------------------------Viral_DNA_Zn_bi-2wazX01 X:394-519                                                                                             ---------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------                               ----------------------------------------------------------------Viral_DNA_Zn_bi-2wazX02 X:394-519                                                                                             ---------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..........eeeee..................eeeeeee.-------------------------------.eeeeeeee.hhhh..............ee.hhhhhhhhhhhhhhhhhhhh........eeeee.....................eeeee.............hhhhhhhhhh.eeeeee......--------......eeehhhhhhhhhhhhhhhhh...............hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2waz X 176 PIVSAWEKGMEAARALMDKYHVDNDLKANFKLLPDQVEALAAVCKTWLNEEHRGLQLTFTSNKTFVTMMGRFLQAYLQSFAEVTYKHHEPTGCALWLHRCAEIEGELKCLHGSIMINKEHVIE-------------------------------QISNTDARCCVHDAACPANQFSGKSCGMFFSEGAKAQVAFKQIKAFMQALYPNAQTGHGHLLMPLRCECNSKPGHAPFLGRQLPKLTPFALSNAEDLDADLISDKSVLASVHHPALIVFQCCNPVY--------GPNCDFKISAPDLLNALVMVRSLWSENFTELPRMVVPEFKWSTKHQYRPVSLPVAHSDARQNPFDF 529
                                   185       195       205       215       225       235       245       255       265       275       285       295  |      -         -         -    |  335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525    
                                                                                                                                                    298                             330                                                                                                                          455      464                                                                 


Chain X from PDB  Type:PROTEIN  Length:315
 aligned with Q6VGU4_ADE05 | Q6VGU4 from UniProtKB/TrEMBL  Length:529

    Alignment length:354
                                   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525    
         Q6VGU4_ADE05   176 PIVSAWEKGMEAARALMDKYHVDNDLKANFKLLPDQVEALAAVCKTWLNEEHRGLQLTFTSNKTFVTMMGRFLQAYLQSFAEVTYKHHEPTGCALWLHRCAEIEGELKCLHGSIMINKEHVIEMDVTSENGQRALKEQSSKAKIVKNRWGRNVVQISNTDARCCVHDAACPANQFSGKSCGMFFSEGAKAQVAFKQIKAFMQALYPNAQTGHGHLLMPLRCECNSKPGHAPFLGRQLPKLTPFALSNAEDLDADLISDKSVLASVHHPALIVFQCCNPVYRNSRAQGGGPNCDFKISAPDLLNALVMVRSLWSENFTELPRMVVPEFKWSTKHQYRNVSLPVAHSDARQNPFDF 529
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2wazX01 X:176-266,X:474-500 Adenovirus Single-stranded Dna-binding Protein, domain 1       2wazX02 X:267-473 Adenovirus Sin                               gle-stranded Dna-binding Protein, domain 2                                                                                                      2wazX01 X:176-266,X:474-500----------------------------- CATH domains
           Pfam domains (1) Viral_DNA_bi-2wazX03 X:176-264                                                           ----------------------------------                               ----------------------------------------------------------------Viral_DNA_Zn_bi-2wazX01 X:394-519                                                                                             ---------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------                               ----------------------------------------------------------------Viral_DNA_Zn_bi-2wazX02 X:394-519                                                                                             ---------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..........eeeee..................eeeeeee.-------------------------------.eeeeeeee.hhhh..............ee.hhhhhhhhhhhhhhhhhhhh........eeeee.....................eeeee.............hhhhhhhhhh.eeeeee......--------......eeehhhhhhhhhhhhhhhhh...............hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2waz X 176 PIVSAWEKGMEAARALMDKYHVDNDLKANFKLLPDQVEALAAVCKTWLNEEHRGLQLTFTSNKTFVTMMGRFLQAYLQSFAEVTYKHHEPTGCALWLHRCAEIEGELKCLHGSIMINKEHVIE-------------------------------QISNTDARCCVHDAACPANQFSGKSCGMFFSEGAKAQVAFKQIKAFMQALYPNAQTGHGHLLMPLRCECNSKPGHAPFLGRQLPKLTPFALSNAEDLDADLISDKSVLASVHHPALIVFQCCNPVY--------GPNCDFKISAPDLLNALVMVRSLWSENFTELPRMVVPEFKWSTKHQYRPVSLPVAHSDARQNPFDF 529
                                   185       195       205       215       225       235       245       255       265       275       285       295  |      -         -         -    |  335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525    
                                                                                                                                                    298                             330                                                                                                                          455      464
   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  (0, 0)

(no "SCOP Domain" information available for 2WAZ)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Viral_DNA_Zn_bi] (2)
(-)
Clan: no clan defined [family: Viral_DNA_bi] (2)

(-) Gene Ontology  (12, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (DNB2_ADE05 | P03265)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
    GO:0045740    positive regulation of DNA replication    Any process that activates or increases the frequency, rate or extent of DNA replication.
    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:0039687    viral DNA strand displacement replication    A viral DNA replication process where only one strand is replicated at once, and which releases a single stranded DNA (ssDNA).
    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:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.

Chain X   (Q6VGU4_ADE05 | Q6VGU4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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
        DNB2_ADE05 | P03265: 1adu 1adv 1anv 2wb0
        Q6VGU4_ADE05 | Q6VGU4: 2wb0

(-) Related Entries Specified in the PDB File

1anv ADENOVIRUS 5 DBP/URANYL FLUORIDE SOAK
2wb0 2.1 RESOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF THE HUMAN ADENOVIRUS 5 SSDNA BINDING PROTEIN