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(-) Description

Title :  TEMPERATURE SENSITIVE D4 MUTANT L110F
 
Authors :  N. Schormann, D. Chattopadhyay
Date :  12 May 16  (Deposition) - 08 Feb 17  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
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 Poxvirus L110F Mutant, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schormann, N. Zhukovskaya, G. Bedwell, M. Nuth, R. Gillilan, P. E. Prevelige, R. P. Ricciardi, S. Banerjee, D. Chattopadhyay
Poxvirus Uracil-Dna Glycosylase-An Unusual Member Of The Family I Uracil-Dna Glycosylases.
Protein Sci. V. 25 2113 2016
PubMed-ID: 27684934  |  Reference-DOI: 10.1002/PRO.3058

(-) 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: UNG, TS17, VACWR109, D4R
    Mutation: YES
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS (STRAIN WESTERN RESERVE)
    Organism Taxid: 10254
    Other Details: TEMPERATURE SENSITIVE D4 MUTANT
    Strain: WESTERN RESERVE
    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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:66 , ASP A:68 , TYR A:70 , PRO A:78 , PHE A:79 , ASN A:120 , HOH A:404binding site for residue GOL A 301
2AC2SOFTWARELYS A:160 , HIS A:181binding site for residue CL A 302
3AC3SOFTWAREGLY B:66 , ASP B:68 , PRO B:69 , PHE B:79 , SER B:88 , ASN B:120 , HIS B:181 , HOH B:410 , HOH B:433binding site for residue GOL B 301
4AC4SOFTWARELYS B:160 , HIS B:181binding site for residue CL B 302
5AC5SOFTWAREGLY C:66 , ILE C:67 , ASP C:68 , PRO C:69 , TYR C:70 , PHE C:79 , ASN C:120 , HOH C:404 , HOH C:414binding site for residue GOL C 301
6AC6SOFTWARELYS C:160 , HIS C:181binding site for residue CL C 302
7AC7SOFTWAREGLY D:66 , ASP D:68 , PRO D:69 , TYR D:70 , PHE D:79 , ASN D:120 , HOH D:409binding site for residue GOL D 301
8AC8SOFTWARELYS D:160 , HIS D:181binding site for residue CL D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JX0)

(-) 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 5JX0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JX0)

(-) Exons   (0, 0)

(no "Exon" information available for 5JX0)

(-) 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:218
                                                                                                                                                                                                                                                          
               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................eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jx0 A   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNFNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


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..............eeeee.............hhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jx0 B   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNFNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    || 172       182       192       202       212      
                                                                                                                                                                                              165|                                                  
                                                                                                                                                                                               168                                                  


Chain C 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......hhhhhhhhhhhhhhhhh....eeeee..............eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jx0 C   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNFNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    || 172       182       192       202       212      
                                                                                                                                                                                              165|                                                  
                                                                                                                                                                                               168                                                  


Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               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......hhhhhhhhhhhhhhhhh....eeeee...........eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jx0 D   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNFNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    || 175       185       195       205       215   
                                                                                                                                                                                              165|                                               
                                                                                                                                                                                               171
   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 5JX0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JX0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JX0)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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        UNG_VACCW | P04303: 2owq 4qcb 5jx3 5jx8

(-) Related Entries Specified in the PDB File

5jx3 5jx8