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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VACCINIA VIRUS DNA POLYMERASE HOLOENZYME SUBUNIT D4 IN COMPLEX WITH THE A20 N-TERMINUS
 
Authors :  C. Contesto-Richefeu, N. Tarbouriech, X. Brazzolotto, W. P. Burmeist F. Iseni
Date :  10 Jan 14  (Deposition) - 26 Mar 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Dna Polymerase Processivity Factor, Dna, Dna Polymerase E9, Hydrolase-Replication Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Contesto-Richefeu, N. Tarbouriech, X. Brazzolotto, S. Betzi, X. Morelli, W. P. Burmeister, F. Iseni
Crystal Structure Of The Vaccinia Virus Dna Polymerase Holoenzyme Subunit D4 In Complex With The A20 N-Terminal Domain.
Plos Pathog. V. 10 03978 2014
PubMed-ID: 24603707  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003978

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: B, A
    EC Number: 3.2.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-DUET1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: D4R, UNG
    Organism Scientific: VACCINIA VIRUS
    Organism Taxid: 10249
    Strain: COPENHAGEN
    Synonym: UDG
 
Molecule 2 - DNA POLYMERASE PROCESSIVITY FACTOR COMPONENT A20
    Chains: D, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-DUET1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL RESIDUES 1-50
    Gene: A20R
    Organism Scientific: VACCINIA VIRUS
    Organism Taxid: 10249
    Strain: COPENHAGEN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:86 , LYS B:87 , HOH B:449BINDING SITE FOR RESIDUE SO4 B 301
2AC2SOFTWARETYR B:70 , PRO B:71 , SER B:88 , HIS B:181 , GOL B:304 , HOH B:417 , HOH B:431BINDING SITE FOR RESIDUE SO4 B 302
3AC3SOFTWAREGLY B:159 , LYS B:160 , THR B:161 , TYR B:180 , HIS B:181 , ALA B:184 , HOH B:401BINDING SITE FOR RESIDUE SO4 B 303
4AC4SOFTWAREGLY B:66 , ASP B:68 , PRO B:78 , PHE B:79 , ASN B:120 , SO4 B:302 , HOH B:402BINDING SITE FOR RESIDUE GOL B 304
5AC5SOFTWARETHR A:85 , LYS A:86 , LYS A:87 , HOH A:413BINDING SITE FOR RESIDUE SO4 A 301
6AC6SOFTWAREGLY A:159 , LYS A:160 , THR A:161 , TYR A:180 , HIS A:181 , ALA A:184 , HOH A:429BINDING SITE FOR RESIDUE SO4 A 302
7AC7SOFTWARETYR A:70 , PRO A:71 , SER A:88 , HIS A:181 , GOL A:304 , HOH A:413 , HOH A:414BINDING SITE FOR RESIDUE SO4 A 303
8AC8SOFTWAREGLY A:66 , ASP A:68 , PRO A:69 , TYR A:70 , PRO A:78 , PHE A:79 , ASN A:120 , SO4 A:303 , HOH A:401BINDING SITE FOR RESIDUE GOL A 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ODA)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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   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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeee..hhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhh....eeeee......hhhhhh....eeeee........hhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oda A  -1 DPMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218


Chain B from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......eeeee..hhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhhh...eeeee.......hhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oda B  -2 QDPMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY 218
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 


Chain C from PDB  Type:PROTEIN  Length:51
                                                                                   
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 4oda C   0 AMTSSADLTNLKELLSLYKSLRFSDSAAIEKYNSLVEWGTSTYWKIGVQKV  50
                                     9        19        29        39        49 


Chain D from PDB  Type:PROTEIN  Length:51
                                                                                   
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 4oda D   0 AMTSSADLTNLKELLSLYKSLRFSDSAAIEKYNSLVEWGTSTYWKIGVQKV  50
                                     9        19        29        39        49
   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 4ODA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 12)

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 Related Entries

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

UniProtKB/Swiss-Prot
        A20_VACCC | P20995: 4od8 4ygm 4yig 5jkr 5jks 5jkt
        UNG_VACCC | P20536: 4od8 4ygm 4yig 5jkr 5jks 5jkt

(-) Related Entries Specified in the PDB File

4od8 A20 T2A MUTANT