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(-) Description

Title :  NUCLEOTIDE MIMICRY IN THE CRYSTAL STRUCTURE OF THE URACIL-DNA GLYCOSYLASE-URACIL GLYCOSYLASE INHIBITOR PROTEIN COMPLEX
 
Authors :  L. H. Pearl, R. Savva
Date :  30 Oct 95  (Deposition) - 08 Mar 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Hydrolase/Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Savva, L. H. Pearl
Nucleotide Mimicry In The Crystal Structure Of The Uracil-Dna Glycosylase-Uracil Glycosylase Inhibitor Protein Complex.
Nat. Struct. Biol. V. 2 752 1995
PubMed-ID: 7552746  |  Reference-DOI: 10.1038/NSB0995-752
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    ChainsE
    EC Number3.2.2.3
    Organism ScientificHERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
    Organism Taxid10299
    Strain17
 
Molecule 2 - URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN
    ChainsI
    Organism ScientificBACILLUS PHAGE PBS1
    Organism Taxid10683
    SynonymUGI

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit EI

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1UDI)

(-) Sites  (0, 0)

(no "Site" information available for 1UDI)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UDI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu E:62 -Pro E:63
2Ala I:62 -Pro I: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  ---  ---EM36L
2UniProtVAR_UNG_HHV11_005 *T280AUNG_HHV11  ---  ---ET190A
   * 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  1E:81-90

(-) Exons   (0, 0)

(no "Exon" information available for 1UDI)

(-) 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 E from PDB  Type:PROTEIN  Length:227
 aligned with UNG_HHV11 | P10186 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:227
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       
            UNG_HHV11   108 DWTTFRRVFLIDDAWRPLMEPELANPLTAHLLAEYNRRCQTEEVLPPREDVFSWTRYCTPDEVRVVIIGQDPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAVKNCYPEARMSGHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARRPGLVFMLWGTHAQNAIRPDPRVHCVLKFSHPSPLSKVPFGTCQHFLVANRYLETRSISPIDWSV 334
               SCOP domains d1udie_ E: Uracil-DNA glycosylase                                                                                                                                                                                                   SCOP domains
               CATH domains 1udiE00 E:18-244 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------UDG-1udiE01 E:73-233                                                                                                                                             ----------- Pfam domains
         Sec.struct. author .hhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhh............hhh.........eeeee........................hhhhhhhhhhhhh............hhhhhh.eeeee.................hhhhhhhhhhhhhhh....eeeee.hhhhhh........eeeee..........hhh..hhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------L---------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1udi E  18 DWTTFRRVFLIDDAWRPLMEPELANPLTAHLLAEYNRRCQTEEVLPPREDVFSWTRYCTPDEVRVVIIGQDPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAVKNCYPEARMSGHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARRPGLVFMLWGTHAQNAIRPDPRVHCVLKFSHPSPLSKVPFGTCQHFLVANRYLETRSISPIDWSV 244
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       

Chain I from PDB  Type:PROTEIN  Length:83
 aligned with UNGI_BPPB2 | P14739 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:83
                                    11        21        31        41        51        61        71        81   
           UNGI_BPPB2     2 TNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
               SCOP domains d1udii_ I: Uracil-DNA glycosylase inhibitor protein                                 SCOP domains
               CATH domains 1udiI00 I:2-84  [code=3.10.450.20, no name defined]                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......eeeee.hhhhhhhh.......eeeeeeee....eeeeeeee......eeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 1udi I   2 TNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
                                    11        21        31        41        51        61        71        81   

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (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.

Chain I   (UNGI_BPPB2 | P14739)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

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    Ala I:62 - Pro I:63   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        UNGI_BPPB2 | P147391eui 1lqg 1lqm 1ugh 1ugi 1uug 2j8x 2ugi 2uug 2zhx 4lyl
        UNG_HHV11 | P101861lau 1udg 1udh 2c53 2c56 4l5n 5ays

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