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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-METHYLADENINE DNA GLYCOSYLASE I (TAG) BOUND TO DNA/3MA
 
Authors :  A. H. Metz, T. Hollis, B. F. Eichman
Date :  03 Jan 07  (Deposition) - 15 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  3-Methyladenine, Dna Repair, Glycosylase, Base Excision, Helix- Hairpin-Helix, 3-Methyladenine Dna Glycosylase I-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. H. Metz, T. Hollis, B. F. Eichman
Dna Damage Recognition And Repair By 3-Methyladenine Dna Glycosylase I (Tag).
Embo J. V. 26 2411 2007
PubMed-ID: 17410210  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601649

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*GP*AP*CP*TP*(3DR)P*AP*CP*GP*GP*G)-3'
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'-D(*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*GP*C)-3'
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - 3-METHYLADENINE DNA GLYCOSYLASE I, CONSTITUTIVE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET19B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTAG
    Organism ScientificSALMONELLA TYPHI
    Organism Taxid601
    Synonym3-METHYLADENINE DNA GLYCOSYLASE I

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2ADK1Ligand/Ion3-METHYL-3H-PURIN-6-YLAMINE
3MSE5Mod. Amino AcidSELENOMETHIONINE
4NA1Ligand/IonSODIUM ION
5ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:4 , HIS A:17 , HIS A:175 , CYS A:179BINDING SITE FOR RESIDUE ZN A 302
2AC2SOFTWARETRP A:117 , VAL A:120 , HOH A:417 , HOH A:418 , HOH A:419BINDING SITE FOR RESIDUE NA A 206
3AC3SOFTWARETYR A:13 , TYR A:16 , TRP A:21 , GLU A:38 , TRP A:46 , ALA A:168 , HOH A:309BINDING SITE FOR RESIDUE ADK A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OFI)

(-) 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:184
 aligned with Q8Z2A5_SALTI | Q8Z2A5 from UniProtKB/TrEMBL  Length:193

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
         Q8Z2A5_SALTI     1 MQRCDWVSQDPLYIAYHDNEWGVPETDSRKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPIRIAAMQEEDVERLLQNTGIIRHRGKIQAIISNARAWLAMEQNGESFADFVWSFVDGQPQITQAASLDKIPTSTPASDALAKALKKRGFKFVGTTICYSFMQACGLVNDHITGCFCHPG 184
               SCOP domains d2ofia_ A: 3-Methyladenine DNA glycosylase I (Tag)                                                                                                                                       SCOP domains
               CATH domains -2ofiA00 A:2-184 Hypothetical protein; domain 2                                                                                                                                          CATH domains
               Pfam domains -----Adenine_glyco-2ofiA01 A:6-184                                                                                                                                                       Pfam domains
         Sec.struct. author .........hhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhhhh......ee....hhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhh..ee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ofi A   1 mQRCDWVSQDPLYIAYHDNEWGVPETDSRKLFEmICLEGQQAGLSWITVLKKRENYRACFHQFDPIRIAAmQEEDVERLLQNTGIIRHRGKIQAIISNARAWLAmEQNGESFADFVWSFVDGQPQITQAASLDKIPTSTPASDALAKALKKRGFKFVGTTICYSFmQACGLVNDHITGCFCHPG 184
                            |       10        20        30   |    40        50        60        70|       80        90       100    |  110       120       130       140       150       160     | 170       180    
                            |                               34-MSE                               71-MSE                           105-MSE                                                      166-MSE              
                            1-MSE                                                                                                                                                                                   

Chain B from PDB  Type:DNA  Length:12
                                            
                 2ofi B   1 CGGACTxACGGG  12
                                  | 10  
                                  7-3DR 

Chain C from PDB  Type:DNA  Length:12
                                            
                 2ofi C   1 CCGTTAGTCCGC  12
                                    10  

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8Z2A5_SALTI | Q8Z2A5)
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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    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: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.

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