Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF MISMATCH SPECIFIC URACIL-DNA GLYCOSYLASE (MUG) FROM DEINOCOCCUS RADIODURANS
 
Authors :  E. Moe, I. Leiros, A. O. Smalas, S. Mcsweeney
Date :  29 Sep 05  (Deposition) - 18 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Deinococcus Radiodurans, Radiation Resistance, Dna Repair Enzymes, Uracil-Dna Glycosylase, Mismatch Specific Dna- Glycosylase, Mug, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Moe, I. Leiros, A. O. Smalas, S. Mcsweeney
The Crystal Structure Of Mismatch Specific Uracil- Dna Glycosylase (Mug) From Deinococcus Radiodurans Reveals A Novel Catalytic Residue And Broad Substrate Specificity
J. Biol. Chem. V. 281 569 2006
PubMed-ID: 16223719  |  Reference-DOI: 10.1074/JBC.M508032200

(-) Compounds

Molecule 1 - G/U MISMATCH-SPECIFIC DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Other Details: ACETATE BOUND IN THE SUBSTRATE POCKET
    Strain: R1
    Synonym: MISMATCH-SPECIFIC URACIL-DNA GLYCOSYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:35 , TYR A:45 , TYR A:46 , ASP A:84 , HOH A:2027 , HOH A:2151 , HOH A:2152BINDING SITE FOR RESIDUE ACT A1190

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C2P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C2P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C2P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C2P)

(-) Exons   (0, 0)

(no "Exon" information available for 2C2P)

(-) 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:183
 aligned with Q9RWF4_DEIRA | Q9RWF4 from UniProtKB/TrEMBL  Length:199

    Alignment length:183
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186   
         Q9RWF4_DEIRA     7 VPDLTGSGEYLVPDVLQPGLTLVLVGTAPSGISARARAYYANPENKFWRTLHAVGLTPRQLVPQEYATLPQYGLGLTDVAKRHSGVDAALPGEAWRPDELRRKVEHYRPRIVAFTSKRGASETLGVPTGKLPYGPQPQPLDWPAETELWVLPSTSPLGHNHFRLEPWQALGDRVRELRGAAEA 189
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeee...hhhhhhhh........hhhhhhhhh.......hhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhh.hhhhh..ee...........eeee....hhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c2p A   7 VPDLTGSGEYLVPDVLQPGLTLVLVGTAPSGISARARAYYANPENKFWRTLHAVGLTPRQLVPQEYATLPQYGLGLTDVAKRHSGVDAALPGEAWRPDELRRKVEHYRPRIVAFTSKRGASETLGVPTGKLPYGPQPQPLDWPAETELWVLPSTSPLGHNHFRLEPWQALGDRVRELRGAAEA 189
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186
   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 2C2P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C2P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C2P)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9RWF4_DEIRA | Q9RWF4)
molecular function
    GO:0019104    DNA N-glycosylase activity    Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
    GO:0008263    pyrimidine-specific mismatch base pair DNA N-glycosylase activity    Catalysis of the removal of mismatched pyrimidine bases in DNA. Enzymes with this activity recognize and remove pyrimidines present in mismatches by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apyrimidinic (AP) site.
    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:0006285    base-excision repair, AP site formation    The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2c2p)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2c2p
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9RWF4_DEIRA | Q9RWF4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.2.2.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9RWF4_DEIRA | Q9RWF4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9RWF4_DEIRA | Q9RWF4: 2c2q

(-) Related Entries Specified in the PDB File

2c2q THE CRYSTAL STRUCTURE OF MISMATCH SPECIFIC URACIL-DNA GLYCOSYLASE (MUG) FROM DEINOCOCCUS RADIODURANS. INACTIVE MUTANT ASP93ALA.