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(-) Description

Title :  STAPHYLOCOCCUS AUREUS UDG / UGI COMPLEX
 
Authors :  H. C. Wang, T. P. Ko, A. H. J. Wang
Date :  18 Jun 13  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Uracil-Dna Glycosylase, Uracil-Dna Glycosylase Inhibitor, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. C. Wang, K. C. Hsu, J. M. Yang, M. L. Wu, T. P. Ko, S. R. Lin, A. H. J. Wang
Staphylococcus Aureus Protein Saugi Acts As A Uracil-Dna Glycosylase Inhibitor.
Nucleic Acids Res. V. 42 1354 2013
PubMed-ID: 24150946  |  Reference-DOI: 10.1093/NAR/GKT964

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    ChainsA
    EC Number3.2.2.27
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneUNG, SAR0586
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid282458
    StrainMRSA252
    SynonymUDG
 
Molecule 2 - UNCHARACTERIZED PROTEIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid1280
    SynonymSAUGI

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3WDG)

(-) Sites  (0, 0)

(no "Site" information available for 3WDG)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:97 -A:214

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:33 -Pro A:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WDG)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_STAAR52-61  1A:52-61

(-) Exons   (0, 0)

(no "Exon" information available for 3WDG)

(-) 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:216
 aligned with UNG_STAAR | Q6GJ88 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
            UNG_STAAR     1 MEWSQIFHDITTKHDFKAMHDFLEKEYSTAIVYPDRENIYQAFDLTPFENIKVVILGQDPYHGPNQAHGLAFSVQPNAKFPPSLRNMYKELADDIGCVRQTPHLQDWAREGVLLLNTVLTVRQGEANSHRDIGWETFTDEIIKAVSDYKEHVVFILWGKPAQQKIKLIDTSKHCIIKSVHPSPLSAYRGFFGSKPYSKANTYLESVGKSPINWCES 216
               SCOP domains d3wdga_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhh........hhhhhhh.eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh.....eeeee...............hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------U_DNA_GLYC----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wdg A   1 MEWSQIFHDITTKHDFKAMHDFLEKEYSTAIVYPDRENIYQAFDLTPFENIKVVILGQDPYHGPNQAHGLAFSVQPNAKFPPSLRNMYKELADDIGCVRQTPHLQDWAREGVLLLNTVLTVRQGEANSHRDIGWETFTDEIIKAVSDYKEHVVFILWGKPAQQKIKLIDTSKHCIIKSVHPSPLSAYRGFFGSKPYSKANTYLESVGKSPINWCES 216
                                    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:110
 aligned with Q936H5_STAAU | Q936H5 from UniProtKB/TrEMBL  Length:112

    Alignment length:110
                                    10        20        30        40        50        60        70        80        90       100       110
         Q936H5_STAAU     1 MTLELQLKHYITNLFNLPKDEKWECESIEEIADDILPDQYVRLGALSNKILQTYTYYSDTLHESNIYPFILYYQKQLIAIGYIDENHDMDFLYLHNTIMPLLDQRYLLTG 110
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.......eeeeeeee.hhh.hhhhh........eeeeeeeehhhhhhh..eeeeeee..eeeeeeee.....eeeeeee....eeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3wdg B   1 MTLELQLKHYITNLFNLPKDEKWECESIEEIADDILPDQYVRLGALSNKILQTYTYYSDTLHESNIYPFILYYQKQLIAIGYIDENHDMDFLYLHNTIMPLLDQRYLLTG 110
                                    10        20        30        40        50        60        70        80        90       100       110

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WDG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WDG)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UNG_STAAR | Q6GJ88)
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B   (Q936H5_STAAU | Q936H5)

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    Tyr A:33 - Pro A:34   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        UNG_STAAR | Q6GJ883wdf
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        Q936H5_STAAU | Q936H55ayr 5ays

(-) Related Entries Specified in the PDB File

3wdf