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(-) Description

Title :  CRYSTAL STRUCTURE OF VACCINIA VIRUS URACIL-DNA GLYCOSYLASE MUTANT R167AD4
 
Authors :  D. Sartmatova, T. Nash, N. Schormann, M. Nuth, R. Ricciardi, S. Banerje D. Chattopadhyay
Date :  09 May 14  (Deposition) - 13 May 15  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dna Repair Enzyme, Component Of Processivity Factor, A20, Dna, Poxvirus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Sartmatova, T. Nash, N. Schormann, M. Nuth, R. Ricciardi, S. Banerjee, D. Chattopadhyay
Crystallization And Preliminary X-Ray Diffraction Analysis Of Three Recombinant Mutants Of Vaccinia Virus Uracil Dna Glycosylase.
Acta Crystallogr. , Sect. F V. 69 295 2013
PubMed-ID: 23519808  |  Reference-DOI: 10.1107/S1744309113002716

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A, B, C, D
    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: ACAM3000_MVA_101, D4, MVA101R, UNG
    Mutation: YES
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS
    Organism Taxid: 126794
    Strain: WESTERN RESERVE, D4R, VACWR109
    Synonym: UDG

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3K1Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:66 , ILE A:67 , ASP A:68 , TYR A:70 , PRO A:78 , PHE A:79 , ASN A:120 , HOH A:412 , HOH A:492 , HOH A:521BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWARELYS A:160 , HIS A:181 , HOH A:526BINDING SITE FOR RESIDUE CL A 302
3AC3SOFTWARESER A:172 , VAL A:174 , HOH A:448 , HOH A:530 , HOH A:541 , HOH B:474BINDING SITE FOR RESIDUE K A 303
4AC4SOFTWARELYS B:160 , TYR B:180 , HIS B:181BINDING SITE FOR RESIDUE CL B 301
5AC5SOFTWAREGLY C:66 , ASP C:68 , TYR C:70 , PRO C:78 , PHE C:79 , SER C:88 , ASN C:120 , HOH C:402 , HOH C:545BINDING SITE FOR RESIDUE GOL C 301
6AC6SOFTWARELYS C:160 , TYR C:180 , HIS C:181 , HOH C:541BINDING SITE FOR RESIDUE CL C 302
7AC7SOFTWAREGLY D:66 , ASP D:68 , TYR D:70 , PRO D:78 , PHE D:79 , SER D:88 , ASN D:120 , HIS D:181 , HOH D:402BINDING SITE FOR RESIDUE GOL D 301
8AC8SOFTWAREALA C:167 , ALA C:168 , LYS C:169 , LEU C:170 , GLU C:171 , ALA D:167 , ALA D:168 , LYS D:169 , LEU D:170 , GLU D:171 , HOH D:481BINDING SITE FOR RESIDUE GOL D 302
9AC9SOFTWARELYS D:160 , TYR D:180 , HIS D:181BINDING SITE FOR RESIDUE CL D 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

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
5Ala C:9 -Pro C:10
6Ser C:43 -Pro C:44
7Ala D:9 -Pro D:10
8Ser D:43 -Pro D:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QCA)

(-) 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:221
                                                                                                                                                                                                                                                             
               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......hhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qca A  -2 GSHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIAAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 


Chain B 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....eeeeehhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qca B  -1 SHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIAAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218


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


Chain D from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               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......hhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhh....eeeee....hhhhh....hhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qca D   0 HMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIAAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
   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 4QCA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UNG_VACCA | Q91UM2: 2owq 3nt7 4dof 4dog 4irb 4lzb 4qc9 5jx3

(-) Related Entries Specified in the PDB File

4dof HIS-TAGGED WILD TYPE VACCINIA VIRUS URACIL-DNA GLYCOSYLASE IN SAME SPACE GROUP
4dog TAG-FREE WILD TYPE VACCINIA VIRUS URACIL-DNA GLYCOSYLASE
4irb DELETION MUTANT OF D4
4lzb VACCINIA VIRUS URACIL-DNA GLYCOSYLASE-URACIL COMPLEX
4qc9
4qcb