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(-) Description

Title :  PROTEIN-DNA COMPLEX OF VACCINIA VIRUS D4 WITH DOUBLE-STRANDED NON-SPECIFIC DNA
 
Authors :  N. Schormann, S. Banerjee, R. Ricciardi, D. Chattopadhyay
Date :  09 May 14  (Deposition) - 10 Jun 15  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,C,D  (1x)
Keywords :  Dna Repair Enzyme, Component Of Processivity Factor, A20, Poxvirus, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schormann, S. Banerjee, R. Ricciardi, D. Chattopadhyay
Binding Of Undamaged Double Stranded Dna To Vaccinia Virus Uracil-Dna Glycosylase
Bmc Struct. Biol. V. 15 10 2015
PubMed: search  |  Reference-DOI: 10.1186/S12900-015-0037-1

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A, B
    EC Number: 3.2.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VACWR109, D4R, UNG
    Mutation: YES
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS
    Organism Taxid: 10254
    Strain: WESTERN RESERVE, D4R, VACWR109
    Synonym: UDG
 
Molecule 2 - 5'-D(*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*C)-3'
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A CD
Biological Unit 2 (1x):  BCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:68 , PRO A:69 , TYR A:70 , PRO A:78 , PHE A:79 , ASN A:120 , HOH A:410BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWAREGLU A:32 , VAL A:33 , TYR A:136 , LYS A:139 , ILE A:140BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWAREILE A:67 , TYR A:122 , ASP A:162 , ILE A:166 , LYS A:169BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWAREASP B:68 , PRO B:69 , TYR B:70 , PRO B:78 , PHE B:79 , ASN B:120 , HOH B:426BINDING SITE FOR RESIDUE GOL B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QCB)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:9 -Pro A:10
2Ser A:43 -Pro A:44
3Ala B:9 -Pro B:10
4Ser B:43 -Pro B:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QCB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QCB)

(-) Exons   (0, 0)

(no "Exon" information available for 4QCB)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeehhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qcb A   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  ||   195       205       215   
                                                                                                                                                                                                                183|                             
                                                                                                                                                                                                                 189                             


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeehhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qcb B   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  ||   195       205       215   
                                                                                                                                                                                                                183|                             
                                                                                                                                                                                                                 189                             


Chain C from PDB  Type:DNA  Length:12
                                            
                 4qcb C   1 GCAAACGTTTGC  12
                                    10  


Chain D from PDB  Type:DNA  Length:10
                                          
                 4qcb D  21 GCAAACGTTT  30
                                    30
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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  (0, 0)

(no "SCOP Domain" information available for 4QCB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QCB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QCB)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  3.2.2.27
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 Related Entries

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

UniProtKB/Swiss-Prot
        UNG_VACCW | P04303: 2owq 5jx0 5jx3 5jx8

(-) Related Entries Specified in the PDB File

4dof HIS-TAGGED WILD TYPE VACCINIA VIRUS URACIL-DNA GLYCOSYLASE
4dog TAG-FREE WILD TYPE VACCINIA VIRUS URACIL-DNA GLYCOSYLASE
4lzb VACCINIA VIRUS URACIL-DNA GLYCOSYLASE-URACIL COMPLEX
4qc9
4qca