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(-) Description

Title :  CRYSTAL STRUCTURE OF VACCINIA VIRUS URACIL DNA GLYCOSYLASE MUTANT DEL171-172D4
 
Authors :  N. Schormann, N. Zhukovskaya, D. Sartmatova, M. Nuth, R. P. Ricciardi, D. Chattopadhyay
Date :  14 Jan 13  (Deposition) - 26 Feb 14  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Uracil-Dna Glycosylase Fold In The Core: 3 Layers (A/B/A); Parallel Beta-Sheet Of 4 Strands In The Order 2134, Beta- Sheets At N- And C- Terminus, Dimeric Assembly, Component Of Processivity Factor, Binding Partners A20 And Dna, Dna Repair Hydrolase, Hydrolase, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schormann, N. Zhukovskaya, D. Sartmatova, M. Nuth, R. P. Ricciardi D. Chattopadhyay
Mutations At The Dimer Interface Affect Both Function And Structure Of The Vaccinia Virus Uracil Dna Glycosylase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) 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: 562
    Expression System Vector Type: PLASMID
    Gene: D4R, VACWR109
    Mutation: YES
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS WESTERN RESERVE
    Organism Taxid: 696871
    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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:159 , LYS A:160 , THR A:161 , TYR A:180 , HIS A:181BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREASP A:68 , PRO A:69 , TYR A:70 , PRO A:78 , PHE A:79 , ASN A:120 , HOH A:433BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWAREGLY B:159 , LYS B:160 , THR B:161 , TYR B:180 , HIS B:181 , ALA B:184BINDING SITE FOR RESIDUE SO4 B 301
4AC4SOFTWAREPRO B:69 , TYR B:70 , PHE B:79 , ASN B:120 , HOH B:430BINDING SITE FOR RESIDUE CL B 302
5AC5SOFTWAREGLY C:159 , LYS C:160 , THR C:161 , GLY C:179 , TYR C:180 , HIS C:181BINDING SITE FOR RESIDUE SO4 C 301
6AC6SOFTWAREGLY D:159 , LYS D:160 , THR D:161 , TYR D:180 , HIS D:181BINDING SITE FOR RESIDUE SO4 D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

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
5Leu B:170 -Pro B:173
6Ala C:9 -Pro C:10
7Ser C:43 -Pro C:44
8Ala D:9 -Pro D:10
9Ser D:43 -Pro D:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IRB)

(-) 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:217
                                                                                                                                                                                                                                                         
               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........eee..eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4irb A  -1 SHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168 ||    181       191       201       211       
                                                                                                                                                                                                     170|                                            
                                                                                                                                                                                                      174                                            


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee......eeeehhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhhh...eeeee........eee...eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4irb B   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170|      182       192       202       212      
                                                                                                                                                                                                   170|                                             
                                                                                                                                                                                                    173                                             


Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeehhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhhh...eeeee.........ee..eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4irb C   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170|      183       193       203       213     
                                                                                                                                                                                                   170|                                            
                                                                                                                                                                                                    174                                            


Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               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........ee..eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4irb D   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       174       184       194       204       214    
                                                                                                                                                                                                  169|                                            
                                                                                                                                                                                                   174
   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 4IRB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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        UNG_VACCA | Q91UM2: 2owq 3nt7 4dof 4dog 4lzb 4qc9 4qca 5jx3

(-) Related Entries Specified in the PDB File

2owq
2owr RELATED ID: R187V RELATED DB: PDB