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(-) Description

Title :  THE NUCLEASE DOMAIN OF ADENO-ASSOCIATED VIRUS REP COMPLEXED WITH THE RBE' STEMLOOP OF THE VIRAL INVERTED TERMINAL REPEAT
 
Authors :  F. Dyda, A. B. Hickman, D. R. Ronning, Z. N. Perez, R. M. Kotin
Date :  10 Jan 04  (Deposition) - 19 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Hydrolase/Dna, Nuclease/Complex, Viral Protein, Nuclease, Replication, Protein-Dna, Stemloop, Helicase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Hickman, D. R. Ronning, Z. N. Perez, R. M. Kotin, F. Dyda
The Nuclease Domain Of Adeno-Associated Virus Rep Coordinates Replication Initiation Using Two Distinct Dna Recognition Interfaces
Mol. Cell V. 13 403 2004
PubMed-ID: 14967147  |  Reference-DOI: 10.1016/S1097-2765(04)00023-1

(-) Compounds

Molecule 1 - REP PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: NUCLEASE DOMAIN, RESIDUES 1-197
    Organism Scientific: ADENO-ASSOCIATED VIRUS 5
    Organism Taxid: 82300
    Other Details: ALL RESIDUES ARE DELETED AFTER S197
    Strain: SEROTYPE 5
 
Molecule 2 - 5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3'
    Chains: C, D
    Fragment: RBE STEMLOOP, RESIDUES 1-15
    Organism Scientific: ADENO-ASSOCIATED VIRUS 5
    Organism Taxid: 82300
    Strain: SEROTYPE 5
    Synthetic: 5'CAGCTCTTTGAGCTG3'

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:82 , HIS A:89 , HIS A:91 , HOH A:2110 , HOH A:2116 , HOH A:2117BINDING SITE FOR RESIDUE MG A1196
2AC2SOFTWAREHOH A:2038 , HOH A:2039 , HOH B:2014 , HOH B:2042 , HOH B:2043BINDING SITE FOR RESIDUE MG A1197
3AC3SOFTWAREGLY A:84 , SER A:85 , GLU A:86 , TYR A:87BINDING SITE FOR RESIDUE CL A1198
4AC4SOFTWAREGLU B:82 , HIS B:89 , HIS B:91 , HOH B:2096 , HOH B:2101 , HOH B:2102BINDING SITE FOR RESIDUE MG B1196
5AC5SOFTWAREDT C:9 , HOH C:2005 , HOH C:2016 , HOH C:2017 , HOH C:2018BINDING SITE FOR RESIDUE MG C1016

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:159 -Pro A:160
2Gln B:159 -Pro B:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UUT)

(-) 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:195
 aligned with Q9YJC1_9VIRU | Q9YJC1 from UniProtKB/TrEMBL  Length:610

    Alignment length:195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     
         Q9YJC1_9VIRU     1 MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVADRIRRVFLYEWNKFSKQESKFFVQFEKGSEYFHLHTLVETSGISSMVLGRYVSQIRAQLVKVVFQGIEPQINDWVAITKVKKGGANKVVDSGYIPAYLLPKVQPELQWAWTNLDEYKLAALNLEERKRLVAQFLAESSQ 195
               SCOP domains d1uuta_ A: Replication protein Rep, nuclease domain                                                                                                                                                 SCOP domains
               CATH domains 1uutA00 A:1-195  [code=3.40.1310.20, no name defined]                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhhh...hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh...........eee..............hhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uut A   1 MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVADRIRRVFLYEWNKFSKQESKFFVQFEKGSEYFHLHTLVETSGISSMVLGRYVSQIRAQLVKVVFQGIEPQINDWVAITKVKKGGANKVVDSGYIPAYLLPKVQPELQWAWTNLDEYKLAALNLEERKRLVAQFLAESSQ 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with Q9YJC1_9VIRU | Q9YJC1 from UniProtKB/TrEMBL  Length:610

    Alignment length:195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     
         Q9YJC1_9VIRU     1 MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVADRIRRVFLYEWNKFSKQESKFFVQFEKGSEYFHLHTLVETSGISSMVLGRYVSQIRAQLVKVVFQGIEPQINDWVAITKVKKGGANKVVDSGYIPAYLLPKVQPELQWAWTNLDEYKLAALNLEERKRLVAQFLAESSQ 195
               SCOP domains d1uutb_ B: Replication protein Rep, nuclease domain                                                                                                                                                 SCOP domains
               CATH domains 1uutB00 B:1-195  [code=3.40.1310.20, no name defined]                                                                                                                                               CATH domains
           Pfam domains (1) ---Rep_N-1uutB01 B:4-189                                                                                                                                                                     ------ Pfam domains (1)
           Pfam domains (2) ---Rep_N-1uutB02 B:4-189                                                                                                                                                                     ------ Pfam domains (2)
         Sec.struct. author ..eeeeeeeee...........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh...........eee...........ee.hhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uut B   1 MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVADRIRRVFLYEWNKFSKQESKFFVQFEKGSEYFHLHTLVETSGISSMVLGRYVSQIRAQLVKVVFQGIEPQINDWVAITKVKKGGANKVVDSGYIPAYLLPKVQPELQWAWTNLDEYKLAALNLEERKRLVAQFLAESSQ 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     


Chain C from PDB  Type:DNA  Length:15
                                               
                 1uut C   1 CAGCTCTTTGAGCTG  15
                                    10     


Chain D from PDB  Type:DNA  Length:15
                                               
                 1uut D   1 CAGCTCTTTGAGCTG  15
                                    10
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Rep_N] (3)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9YJC1_9VIRU | Q9YJC1)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9YJC1_9VIRU | Q9YJC1: 1m55 1rz9

(-) Related Entries Specified in the PDB File

1m55 CATALYTIC DOMAIN OF THE ADENO ASSOCIATED VIRUS TYPE 5 REPPROTEIN