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(-) Description

Title :  SOLUTION NMR STRUCTURE OF A PUTATIVE URACIL DNA GLYCOSYLASE FROM METHANOSARCINA ACETIVORANS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET MVR76
 
Authors :  J. M. Aramini, K. Hamilton, C. T. Ciccosanti, H. Wang, H. W. Lee, B. Rost, T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione, Northeast Struc Genomics Consortium (Nesg)
Date :  13 Sep 10  (Deposition) - 20 Oct 10  (Release) - 22 Feb 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Structural Genomics, Northeast Structural Genomics Consortium (Nesg), Psi-Biology, Protein Structure Initiative, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Aramini, K. Hamilton, C. T. Ciccosanti, H. Wang, H. W. Lee, B. Rost T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione
Solution Nmr Structure Of A Putative Uracil Dna Glycosylase From Methanosarcina Acetivorans, Northeast Structural Genomics Consortium Target Mvr76
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)PMGK
    Expression System Taxid: 469008
    Expression System Vector: PET21
    Gene: MA_0462
    Organism Scientific: METHANOSARCINA ACETIVORANS
    Organism Taxid: 2214

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2L3F)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:161
 aligned with HDG_METAC | Q8TTH3 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:161
                                                                                                                                                                                       158   
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       | - 
            HDG_METAC     1 MIKRGFPAVLDENTEILILGSLPSDESIRKQQYYGNPGNDFWRLVGHAIGENLQDMAYEKKLKTLKHNRIGLWDVFKAGSREGSQDSKIGDEEINDFSGLKEMVPKLRLICFNGRKAGEYEPLLRGMGYETKVLPSSSGANRRFSKNRESEWEAVFRH---   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...........eeeee...hhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhhhhhhhh.eeeee.eeee.............ee....hhhhhh....eeeeehhhhhhhhhhhhhhh.eeeee...hhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2l3f A   1 MIKRGFPAVLDENTEILILGSLPSDESIRKQQYYGNPGNDFWRLVGHAIGENLQDMAYEKKLKTLKHNRIGLWDVFKAGSREGSQDSKIGDEEINDFSGLKEMVPKLRLICFNGRKAGEYEPLLRGMGYETKVLPSSSGANRRFSKNRESEWEAVFRHLEH 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
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  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 2L3F)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2L3F)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A   (HDG_METAC | Q8TTH3)
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.

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