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(-) Description

Title :  CATALYTIC DOMAIN OF THE ADENO ASSOCIATED VIRUS TYPE 5 REP PROTEIN
 
Authors :  A. B. Hickman, D. R. Ronning, R. M. Kotin, F. Dyda
Date :  08 Jul 02  (Deposition) - 28 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Endonuclease, Rep, Rolling Circle Replication, Adeno- Associated Virus, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Hickman, D. R. Ronning, R. M. Kotin, F. Dyda
Structural Unity Among Viral Origin Binding Proteins: Crystal Structure Of The Nuclease Domain Of Adeno-Associated Virus Rep.
Mol. Cell V. 10 327 2002
PubMed-ID: 12191478  |  Reference-DOI: 10.1016/S1097-2765(02)00592-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REP PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (RESIDUES 1-197)
    Organism Scientific: ADENO-ASSOCIATED VIRUS - 5
    Organism Taxid: 82300
    Synonym: ADENO-ASSOCIATED VIRUS 5

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:82 , HIS B:89 , HIS B:91BINDING SITE FOR RESIDUE ZN B 201
2AC2SOFTWAREGLU A:82 , HIS A:89 , HIS A:91BINDING SITE FOR RESIDUE ZN A 202
3AC3SOFTWAREGLU B:16 , HOH B:1376BINDING SITE FOR RESIDUE ZN B 203
4AC4SOFTWAREGLN B:73 , GLU B:95 , HOH B:1057 , HOH B:1058 , HOH B:1059 , HOH B:1329BINDING SITE FOR RESIDUE ZN B 204
5AC5SOFTWAREGLN A:73 , GLU A:95 , HOH A:1011 , HOH A:1211BINDING SITE FOR RESIDUE ZN A 205
6AC6SOFTWAREASP B:146BINDING SITE FOR RESIDUE ZN B 206
7AC7SOFTWARESER A:85 , GLU A:86 , TYR A:87BINDING SITE FOR RESIDUE CL A 301
8AC8SOFTWARESER B:85 , GLU B:86 , TYR B:87BINDING SITE FOR RESIDUE CL B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M55)

(-) 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 1M55)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M55)

(-) Exons   (0, 0)

(no "Exon" information available for 1M55)

(-) 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:193
 aligned with Q9YJC1_9VIRU | Q9YJC1 from UniProtKB/TrEMBL  Length:610

    Alignment length:193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
         Q9YJC1_9VIRU     1 MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVADRIRRVFLYEWNKFSKQESKFFVQFEKGSEYFHLHTLVETSGISSMVLGRYVSQIRAQLVKVVFQGIEPQINDWVAITKVKKGGANKVVDSGYIPAYLLPKVQPELQWAWTNLDEYKLAALNLEERKRLVAQFLAES 193
               SCOP domains d1m55a_ A: Replication protein Rep, nuclease domain                                                                                                                                               SCOP domains
               CATH domains 1m55A00 A:1-193  [code=3.40.1310.20, no name defined]                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee............hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh...........eee...........ee.hhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m55 A   1 MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVADRIRRVFLYEWNKFSKQESKFFVQFEKGSEYFHLHTLVETSGISSMVLGRYVSQIRAQLVKVVFQGIEPQINDWVAITKVKKGGANKVVDSGYIPAYLLPKVQPELQWAWTNLDEYKLAALNLEERKRLVAQFLAES 193
                                    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:193
 aligned with Q9YJC1_9VIRU | Q9YJC1 from UniProtKB/TrEMBL  Length:610

    Alignment length:193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
         Q9YJC1_9VIRU     1 MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVADRIRRVFLYEWNKFSKQESKFFVQFEKGSEYFHLHTLVETSGISSMVLGRYVSQIRAQLVKVVFQGIEPQINDWVAITKVKKGGANKVVDSGYIPAYLLPKVQPELQWAWTNLDEYKLAALNLEERKRLVAQFLAES 193
               SCOP domains d1m55b_ B: Replication protein Rep, nuclease domain                                                                                                                                               SCOP domains
               CATH domains 1m55B00 B:1-193  [code=3.40.1310.20, no name defined]                                                                                                                                             CATH domains
           Pfam domains (1) ---Rep_N-1m55B01 B:4-189                                                                                                                                                                     ---- Pfam domains (1)
           Pfam domains (2) ---Rep_N-1m55B02 B:4-189                                                                                                                                                                     ---- Pfam domains (2)
         Sec.struct. author ..eeeeeeee............hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh...........eee...........ee.hhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m55 B   1 MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVADRIRRVFLYEWNKFSKQESKFFVQFEKGSEYFHLHTLVETSGISSMVLGRYVSQIRAQLVKVVFQGIEPQINDWVAITKVKKGGANKVVDSGYIPAYLLPKVQPELQWAWTNLDEYKLAALNLEERKRLVAQFLAES 193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   Legend:   → Mismatch (orange background)
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  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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  1m55
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 Related Entries

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

UniProtKB/TrEMBL
        Q9YJC1_9VIRU | Q9YJC1: 1rz9 1uut

(-) Related Entries Specified in the PDB File

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