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(-) Description

Title :  A COMPARATIVE STUDY OF URACIL DNA GLYCOSYLASES FROM HUMAN AND HERPES SIMPLEX VIRUS TYPE 1
 
Authors :  K. Krusong, E. P. Carpenter, S. R. W. Bellamy, R. Savva, G. S. Baldwin
Date :  25 Oct 05  (Deposition) - 28 Nov 05  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Uracil Dna Glycosylase, Dna Repair, Dna Damage, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Krusong, E. P. Carpenter, S. R. W. Bellamy, R. Savva, G. S. Baldwin
A Comparative Study Of Uracil-Dna Glycosylases From Human And Herpes Simplex Virus Type 1.
J. Biol. Chem. V. 281 4983 2006
PubMed-ID: 16306042  |  Reference-DOI: 10.1074/JBC.M509137200

(-) Compounds

Molecule 1 - URACIL DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: D88N/H20N
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PTRC99A
    Mutation: YES
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1DUR1Ligand/Ion2'-DEOXYURIDINE
2GOL4Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:86 , GLN A:87 , ASN A:88 , TYR A:90 , ALA A:100 , PHE A:101 , SER A:112 , ASN A:147 , SER A:212 , PRO A:213 , HOH A:2257 , HOH A:2258 , HOH A:2259 , HOH A:2260 , HOH A:2261BINDING SITE FOR RESIDUE DUR A1245
2AC2SOFTWARELEU A:214 , LYS A:216 , HOH A:2263BINDING SITE FOR RESIDUE GOL A1246
3AC3SOFTWAREASN A:115 , PRO A:218 , PHE A:219 , GLY A:220 , HOH A:2264 , HOH A:2266BINDING SITE FOR RESIDUE GOL A1247
4AC4SOFTWAREARG A:197 , ASP A:199 , PRO A:200 , HOH A:2269BINDING SITE FOR RESIDUE GOL A1248
5AC5SOFTWAREPRO A:181 , ARG A:235 , ILE A:237BINDING SITE FOR RESIDUE GOL A1249

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C53)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:62 -Pro A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_UNG_HHV11_004 *M126LUNG_HHV11  ---  ---AM36L
2UniProtVAR_UNG_HHV11_005 *T280AUNG_HHV11  ---  ---AT190A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_HHV11171-180  1A:81-90

(-) Exons   (0, 0)

(no "Exon" information available for 2C53)

(-) 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:228
 aligned with UNG_HHV11 | P10186 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:228
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        
            UNG_HHV11   107 LDWTTFRRVFLIDDAWRPLMEPELANPLTAHLLAEYNRRCQTEEVLPPREDVFSWTRYCTPDEVRVVIIGQDPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAVKNCYPEARMSGHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARRPGLVFMLWGTHAQNAIRPDPRVHCVLKFSHPSPLSKVPFGTCQHFLVANRYLETRSISPIDWSV 334
               SCOP domains d2c53a_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains 2c53A00 A:17-244 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhh.hhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhhh.eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhh.......eeeee..............hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------L---------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c53 A  17 LDWTTFRRVFLIDDAWRPLMEPELANPLTAHLLAEYNRRCQTEEVLPPREDVFSWTRYCTPDEVRVVIIGQNPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAVKNCYPEARMSGHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARRPGLVFMLWGTHAQNAIRPDPRVHCVLKFSNPSPLSKVPFGTCQHFLVANRYLETRSISPIDWSV 244
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C53)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UNG_HHV11 | P10186)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0004844    uracil DNA N-glycosylase activity    Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  2c53
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  UNG_HHV11 | P10186
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  3.2.2.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        UNG_HHV11 | P10186: 1lau 1udg 1udh 1udi 2c56 4l5n 5ays

(-) Related Entries Specified in the PDB File

1lau URACIL-DEOXYRIBONUCLEIC ACID GLYCOSYLASE
1udg MOL_ID: 1; MOLECULE: URACIL-DEOXYRIBONUCLEIC ACID GLYCOSYLASE; CHAIN: NULL; EC: 3.2.2. 3; OTHER_DETAILS: ENCODED BY THE UL2 ORF OF HERPES SIMPLEX VIRUS TYPE 1
1udh MOL_ID: 1; MOLECULE: URACIL-DEOXYRIBONUCLEIC ACID GLYCOSYLASE; CHAIN: NULL; EC: 3.2.2. 3; HETEROGEN: URACIL; OTHER_DETAILS: ENCODED BY THE UL2 ORF OF HERPES SIMPLEX VIRUS TYPE 1
1udi NUCLEOTIDE MIMICRY IN THE CRYSTAL STRUCTURE OF THE URACIL-DNA GLYCOSYLASE - URACIL GLYCOSYLASE INHIBITOR PROTEIN COMPLEX
2c56 A COMPARATIVE STUDY OF URACIL DNA GLYCOSYLASES FROM HUMAN AND HERPES SIMPLEX VIRUS TYPE 1