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(-) Description

Title :  NEW IMPROVED STRUCTURE OF D4 IN TRIGONAL SPACE GROUP
 
Authors :  N. Schormann, D. Chattopadhyay
Date :  12 May 16  (Deposition) - 08 Feb 17  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Repair Enzyme Component Of Processivity Factor Poxvirus, 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
    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
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS (STRAIN WESTERN RESERVE)
    Organism Taxid: 10254
    Strain: WESTERN RESERVE
    Synonym: UDG

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:160 , THR A:161 , TYR A:180 , HIS A:181 , HOH A:459 , HOH A:476binding site for residue SO4 A 301
2AC2SOFTWAREVAL A:4 , THR A:5 , HOH A:426 , HOH A:432 , ILE B:112binding site for residue SO4 A 302
3AC3SOFTWAREGLY A:-2 , PRO A:-4 , ARG A:-3 , SER A:-1 , HIS A:0 , HOH A:409binding site for residue GOL A 303
4AC4SOFTWAREASP A:68 , PRO A:69 , TYR A:70 , PRO A:78 , PHE A:79 , ASN A:120 , HOH A:421 , HOH A:452binding site for residue GOL A 304
5AC5SOFTWARELYS B:160 , THR B:161 , TYR B:180 , HIS B:181 , HOH B:441binding site for residue SO4 B 301
6AC6SOFTWAREASP B:68 , PRO B:69 , TYR B:70 , PHE B:79 , ASN B:120binding site for residue GOL B 302
7AC7SOFTWARELYS B:87 , HOH B:448binding site for residue GOL B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JX8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JX8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JX8)

(-) Exons   (0, 0)

(no "Exon" information available for 5JX8)

(-) Sequences/Alignments

Asymmetric/Biological 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:227
                                                                                                                                                                                                                                                                   
               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................eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jx8 A  -8 SGLVPRGSHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       


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..hhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh....eeeeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh.eeeeee....ee......hhhhhhhhhhhhhhhhhhhh.eeeee................eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jx8 B  -2 GSHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217
   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 5JX8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JX8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JX8)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:9 - Pro A:10   [ RasMol ]  
    Ala B:9 - Pro B:10   [ RasMol ]  
    Ser A:43 - Pro A:44   [ RasMol ]  
    Ser B:43 - Pro B:44   [ RasMol ]  
 

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  3.2.2.27
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 Related Entries

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

UniProtKB/Swiss-Prot
        UNG_VACCW | P04303: 2owq 4qcb 5jx0 5jx3

(-) Related Entries Specified in the PDB File

5jx0 5jx3