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(-) Description

Title :  SOLUTION STRUCTURE AND BASE PERTURBATION STUDIES REVEAL A NOVEL MODE OF ALKYLATED BASE RECOGNITION BY 3-METHYLADENINE DNA GLYCOSYLASE I
 
Authors :  C. Cao, K. Kwon, Y. L. Jiang, A. C. Drohat, J. T. Stivers
Date :  02 May 03  (Deposition) - 25 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (25x)
Keywords :  3-Methyladenine Tag Complex Nmr, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Cao, K. Kwon, Y. L. Jiang, A. C. Drohat, J. T. Stivers
Solution Structure And Base Perturbation Studies Reveal A Novel Mode Of Alkylated Base Recognition By 3-Methyladenine Dna Glycosylase I
J. Biol. Chem. V. 278 48012 2003
PubMed-ID: 13129925  |  Reference-DOI: 10.1074/JBC.M307500200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA-3-METHYLADENINE GLYCOSYLASE I
    Chains: A
    EC Number: 3.2.2.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: STRAIN B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TAG OR B3549
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  
NMR Structure (25x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

NMR Structure (2, 2)
No.NameCountTypeFull Name
1ADK1Ligand/Ion3-METHYL-3H-PURIN-6-YLAMINE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:4 , HIS A:17 , HIS A:175 , CYS A:179BINDING SITE FOR RESIDUE ZN A 188
2AC2SOFTWARETRP A:6 , TYR A:13 , TYR A:16 , TRP A:21 , GLU A:38 , TRP A:46 , SER A:164BINDING SITE FOR RESIDUE ADK A 189

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P7M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P7M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P7M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P7M)

(-) Exons   (0, 0)

(no "Exon" information available for 1P7M)

(-) 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    
   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:187
 aligned with 3MG1_ECOLI | P05100 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
           3MG1_ECOLI     1 MERCGWVSQDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPFVDFVWSFVNHQPQVTQATTLSEIPTSTSASDALSKALKKRGFKFVGTTICYSFMQACGLVNDHVVGCCCYPGNKP 187
               SCOP domains d1p7ma_ A: 3-Methyladenine DNA glycosylase I (Tag)                                                                                                                                          SCOP domains
               CATH domains 1p7mA00 A:1-187 Hypothetical protein; domain 2                                                                                                                                              CATH domains
               Pfam domains -----Adenine_glyco-1p7mA01 A:6-184                                                                                                                                                      --- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....ee....hhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.ee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p7m A   1 MERCGWVSQDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPFADFVWSFVNHQPQMTQATTLSEIPTSTPASDALSKALKKRGFKFVGTTICYSFMQACGLVNDHVVGCCCYPGNKP 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: Adenine_glyco] (4)

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (3MG1_ECOLI | P05100)
molecular function
    GO:0008725    DNA-3-methyladenine glycosylase activity    Catalysis of the reaction: DNA containing 3-methyladenine + H2O = DNA with abasic site + 3-methyladenine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methyladenine and the deoxyribose sugar to remove the 3-methyladenine, leaving an abasic site.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        3MG1_ECOLI | P05100: 1lmz 1nku

(-) Related Entries Specified in the PDB File

1lmz SOLUTION STRUCTURE OF 3-METHYLADENINE DNA GLYCOSYLASE I (TAG)
1nku NMR SOLUTION STRUCTURE OF ZINC-BINDING PROTEIN 3- METHYLADENINE DNA GLYCOSYLASE I (TAG)