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(-) Description

Title :  VACCINIA VIRUS HIS-D4/A20(1-50) IN COMPLEX WITH URACIL
 
Authors :  N. Tarbouriech, F. Iseni, W. P. Burmeister
Date :  26 Feb 15  (Deposition) - 10 Jun 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Uracil Dna Glycosidase, Virus Replication, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. P. Burmeister, N. Tarbouriech, P. Fender, C. Contesto-Richefeu, C. N. Peyrefitte, F. Iseni
Crystal Structure Of The Vaccinia Virus Uracil-Dna Glycosylase In Complex With Dna.
J. Biol. Chem. V. 290 17923 2015
PubMed-ID: 26045555  |  Reference-DOI: 10.1074/JBC.M115.648352

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: B, A
    EC Number: 3.2.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: UNG, D4R
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS (STRAIN COPENHAGEN)
    Organism Taxid: 10249
    Strain: COPENHAGEN
    Synonym: UDG
 
Molecule 2 - DNA POLYMERASE PROCESSIVITY FACTOR COMPONENT A20
    Chains: D, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 1-50
    Gene: A20R
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS (STRAIN COPENHAGEN)
    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, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
2URA2Ligand/IonURACIL
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2URA1Ligand/IonURACIL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2URA1Ligand/IonURACIL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:70 , PRO B:71 , SER B:88 , HIS B:181 , SO4 B:302 , URA B:305 , HOH B:406 , HOH B:417 , HOH B:467binding site for residue SO4 B 301
2AC2SOFTWARELYS B:86 , LYS B:87 , SO4 B:301 , HOH B:406 , HOH B:417 , HOH B:461 , HOH B:487binding site for residue SO4 B 302
3AC3SOFTWAREGLY B:159 , LYS B:160 , THR B:161 , TYR B:180 , HIS B:181 , HOH B:420binding site for residue SO4 B 303
4AC4SOFTWAREASN B:83 , THR B:85 , HOH B:464 , HOH B:507 , HOH B:509binding site for residue SO4 B 304
5AC5SOFTWAREGLY B:66 , ILE B:67 , ASP B:68 , TYR B:70 , PRO B:78 , PHE B:79 , ASN B:120 , SO4 B:301 , HOH B:459 , HOH B:512binding site for residue URA B 305
6AC6SOFTWARETYR A:70 , PRO A:71 , SER A:88 , HIS A:181 , URA A:304 , HOH A:407 , HOH A:412 , HOH A:481binding site for residue SO4 A 301
7AC7SOFTWARELYS A:86 , LYS A:87 , HOH A:407 , HOH A:440 , HOH A:481binding site for residue SO4 A 302
8AC8SOFTWAREGLY A:159 , LYS A:160 , THR A:161 , TYR A:180 , HIS A:181 , ALA A:184 , HOH A:441binding site for residue SO4 A 303
9AC9SOFTWAREGLY A:66 , ILE A:67 , ASP A:68 , TYR A:70 , PRO A:78 , PHE A:79 , ASN A:120 , SO4 A:301 , HOH A:490 , HOH A:494binding site for residue URA A 304

(-) SS Bonds  (0, 0)

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

(-) 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 4YGM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YGM)

(-) 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:220
                                                                                                                                                                                                                                                            
               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......hhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ygm 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:218
                                                                                                                                                                                                                                                          
               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...eeeee......hhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ygm B   1 MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


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
                 4ygm C   0 AMTSSADLTNLKELLSLYKSLRFSDSAAIEKYNSLVEWGTSTYWKIGVQKV  50
                                     9        19        29        39        49 


Chain D from PDB  Type:PROTEIN  Length:50
                                                                                  
               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
                 4ygm D   1 MTSSADLTNLKELLSLYKSLRFSDSAAIEKYNSLVEWGTSTYWKIGVQKV  50
                                    10        20        30        40        50
   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 4YGM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4oda 4yig 5jkr 5jks 5jkt
        UNG_VACCC | P20536: 4od8 4oda 4yig 5jkr 5jks 5jkt

(-) Related Entries Specified in the PDB File

4od8 MR MODEL