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(-) Description

Title :  CRYSTAL STRUCTURE OF AAV2 REP40-ADP COMPLEX
 
Authors :  J. A. James, A. K. Aggarwal, R. M. Linden, C. R. Escalante
Date :  13 Jul 04  (Deposition) - 24 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Aaa+ Protein, P-Loop Atpases, Helicase, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. James, A. K. Aggarwal, R. M. Linden, C. R. Escalante
Structure Of Adeno-Associated Virus Type 2 Rep40-Adp Complex: Insight Into Nucleotide Recognition And Catalysis By Superfamily 3 Helicases
Proc. Natl. Acad. Sci. Usa V. 101 12455 2004
PubMed-ID: 15310852  |  Reference-DOI: 10.1073/PNAS.0403454101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA REPLICATION PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(PLYSS)DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HELICASE DOMAIN 225-490
    Gene: REP
    Organism Scientific: ADENO-ASSOCIATED VIRUS - 2
    Organism Taxid: 10804
    Synonym: NONCAPSID PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:26 , HOH A:40 , HOH A:78 , HOH A:93 , HOH A:110 , HOH A:112 , ALA A:336 , THR A:337 , THR A:338 , GLY A:339 , LYS A:340 , THR A:341 , ASN A:342 , LEU A:454 , ASP A:455 , HIS A:456 , PHE A:458 , GLY A:459 , LYS A:460BINDING SITE FOR RESIDUE ADP A 491

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U0J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U0J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U0J)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SF3_HELICASE_1PS51206 Superfamily 3 helicase of DNA viruses domain profile.REP68_AAV2S308-463  1A:308-463

(-) Exons   (0, 0)

(no "Exon" information available for 1U0J)

(-) 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 A from PDB  Type:PROTEIN  Length:261
 aligned with REP68_AAV2S | P03132 from UniProtKB/Swiss-Prot  Length:536

    Alignment length:267
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       
          REP68_AAV2S   224 YMELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLVGQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGG 490
               SCOP domains d1u0ja_ A: Rep 40 protein helicase domain                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhh..eee.........hhhhh...eeee....ee..hhhhhhhhhh...ee.------..ee....eeeee......eee..eee..hhhhhhh.eeeee............hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------SF3_HELICASE_1  PDB: A:308-463 UniProt: 308-463                                                                                                             --------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u0j A 224 GMELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLVGQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSKVRV------SAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGG 490
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       | -    |  413       423       433       443       453       463       473       483       
                                                                                                                                                                                                           401    408
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1U0J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1U0J)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (REP68_AAV2S | P03132)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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: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:0039645    modulation by virus of host G1/S transition checkpoint    Any viral process that modulates the frequency, rate or extent of the host cell G1/S transition checkpoint.
    GO:0060153    modulation by virus of host cell cycle    Any viral process that modulates the rate or extent of progression through the cell cycle.
    GO:0039665    permeabilization of host organelle membrane involved in viral entry into host cell    Induction of organellar membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with a viral capsid. Results in release of the virus contents from an organelle into the host cell cytoplasm.
    GO:0039592    suppression by virus of G2/M transition of host mitotic cell cycle    Any viral process that decreases the rate or extent of progression from G2 phase to M phase of the host mitotic cell cycle.
    GO:0039693    viral DNA genome replication    The replication of a viral DNA genome.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        REP68_AAV2S | P03132: 1s9h 4zo0 4zq9 5dcx

(-) Related Entries Specified in the PDB File

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