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(-) Description

Title :  THE CRYSTAL STRUCTURE OF URACIL-DNA N-GLYCOSYLASE (UNG) FROM DEINOCOCCUS RADIODURANS.
 
Authors :  I. Leiros, E. Moe, A. O. Smalas, S. Mcsweeney
Date :  13 Apr 05  (Deposition) - 27 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Base Excision Repair, Radiation Resistance, Dna Damage, Dna Repair, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Leiros, E. Moe, A. O. Smalas, S. Mcsweeney
Structure Of The Uracil-Dna N-Glycosylase (Ung) From Deinococcus Radiodurans.
Acta Crystallogr. , Sect. D V. 61 1049 2005
PubMed-ID: 16041069  |  Reference-DOI: 10.1107/S090744490501382X

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Other Details: RESIDUES 1-16 AND 247 NOT VISIBLE IN ELECTRON DENSITY
    Strain: R1
    Synonym: UDG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1NO33Ligand/IonNITRATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:82 , ASP A:83 , SER A:95 , PHE A:96 , ASN A:142 , HOH A:2154BINDING SITE FOR RESIDUE NO3 A1247
2AC2SOFTWAREGLY A:184 , SER A:185 , ARG A:188 , SER A:204 , GLY A:205 , LEU A:210 , SER A:211 , GLN A:213 , TYR A:214BINDING SITE FOR RESIDUE NO3 A1248
3AC3SOFTWARELEU A:47 , ARG A:51 , VAL A:63BINDING SITE FOR RESIDUE NO3 A1249

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:57 -Pro A:58
2Val A:244 -Thr A:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BOO)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_DEIRA76-85  1A:76-85

(-) Exons   (0, 0)

(no "Exon" information available for 2BOO)

(-) 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:230
 aligned with UNG_DEIRA | Q9RWH9 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:230
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
            UNG_DEIRA    17 PIIPANLPEDWQEALLPEFSAPYFHELTDFLRQERKEYTIYPPAPDVFNALRYTPLGEVKVLILGQDPYHGPNQAHGLSFSVRPGVRVPPSLRNIYKELTEDIPGFVAPKHGYLRSWAEQGVLLLNAVLTVRAGQANSHQGKGWEHFTDAVIKAVNAKEERVVFILWGSYARKKKKLITGKNHVVIESGHPSPLSEQYFFGTRPFSKTNEALEKAGRGPVEWQLPATVTE 246
               SCOP domains d2booa_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains 2booA00 A:17-246 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee....ee..........hhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhh.....eeeee......hhhhh...hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------U_DNA_GLYC----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2boo A  17 PIIPANLPEDWQEALLPEFSAPYFHELTDFLRQERKEYTIYPPAPDVFNALRYTPLGEVKVLILGQDPYHGPNQAHGLSFSVRPGVRVPPSLRNIYKELTEDIPGFVAPKHGYLRSWAEQGVLLLNAVLTVRAGQANSHQGKGWEHFTDAVIKAVNAKEERVVFILWGSYARKKKKLITGKNHVVIESGHPSPLSEQYFFGTRPFSKTNEALEKAGRGPVEWQLPATVTE 246
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
   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
(-)
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 2BOO)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UNG_DEIRA | Q9RWH9)
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.

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 Related Entries

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UniProtKB/Swiss-Prot
        UNG_DEIRA | Q9RWH9: 3ufm 4uqm

(-) Related Entries Specified in the PDB File

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