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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-METHYLADENINE DNA GLYCOSYLASE I (TAG)
 
Authors :  A. H. Metz, T. Hollis, B. F. Eichman
Date :  03 Jan 07  (Deposition) - 15 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  3-Methyladenine, Dna Repair, Glycosylase, Base Excision, Helix-Hairpin-Helix, Hydrolase (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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-METHYLADENINE DNA GLYCOSYLASE I, CONSTITUTIVE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TAG
    Organism Scientific: SALMONELLA TYPHI
    Organism Taxid: 601
    Synonym: 3-METHYLADENINE DNA GLYCOSYLASE I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1PGE8Ligand/IonTRIETHYLENE GLYCOL
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1PGE4Ligand/IonTRIETHYLENE GLYCOL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1PGE4Ligand/IonTRIETHYLENE GLYCOL
2ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:4 , HIS A:17 , HIS A:175 , CYS A:179BINDING SITE FOR RESIDUE ZN A 201
02AC2SOFTWARECYS B:4 , HIS B:17 , HIS B:175 , CYS B:179BINDING SITE FOR RESIDUE ZN B 201
03AC3SOFTWARETRP A:6 , TYR A:13 , TYR A:16 , GLU A:38 , TRP A:46 , LEU A:132 , SER A:164 , GLN A:167 , ALA A:168 , HOH A:949 , GLN B:81 , ARG B:87 , HOH B:923BINDING SITE FOR RESIDUE PGE A 701
04AC4SOFTWAREGLN A:81 , ARG A:87 , TRP B:6 , TYR B:13 , GLU B:38 , TRP B:46 , SER B:164 , ALA B:168 , HOH B:921 , HOH B:991BINDING SITE FOR RESIDUE PGE B 801
05AC5SOFTWAREMET B:71 , GLN B:72 , GLN B:93 , ILE B:96 , SER B:97 , ARG B:100BINDING SITE FOR RESIDUE PGE B 901
06AC6SOFTWAREASP B:114 , TRP B:117 , GLY B:122BINDING SITE FOR RESIDUE PGE B 902
07AC7SOFTWAREILE A:96 , SER A:97 , ARG A:100BINDING SITE FOR RESIDUE PGE A 903
08AC8SOFTWARETHR A:26 , ASP A:114 , TRP A:117BINDING SITE FOR RESIDUE PGE A 904
09AC9SOFTWAREASP A:133 , LYS A:134BINDING SITE FOR RESIDUE PGE A 905
10BC1SOFTWAREARG A:78 , GLN B:41 , ALA B:42 , GLY B:43 , LEU B:44 , HOH B:957 , HOH B:993BINDING SITE FOR RESIDUE PGE B 906

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OFK)

(-) Sequences/Alignments

Asymmetric 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:182
 aligned with Q8Z2A5_SALTI | Q8Z2A5 from UniProtKB/TrEMBL  Length:193

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
         Q8Z2A5_SALTI     2 QRCDWVSQDPLYIAYHDNEWGVPETDSRKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPIRIAAMQEEDVERLLQNTGIIRHRGKIQAIISNARAWLAMEQNGESFADFVWSFVDGQPQITQAASLDKIPTSTPASDALAKALKKRGFKFVGTTICYSFMQACGLVNDHITGCFCHP 183
               SCOP domains d2ofka_ A: 3-Methyladenine DNA glycosylase I (Tag)                                                                                                                                     SCOP domains
               CATH domains 2ofkA00 A:2-183 Hypothetical protein; domain 2                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.....ee....hhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhh..ee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ofk A   2 QRCDWVSQDPLYIAYHDNEWGVPETDSRKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPIRIAAMQEEDVERLLQNTGIIRHRGKIQAIISNARAWLAMEQNGESFADFVWSFVDGQPQITQAASLDKIPTSTPASDALAKALKKRGFKFVGTTICYSFMQACGLVNDHITGCFCHP 183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  


Chain B from PDB  Type:PROTEIN  Length:183
 aligned with Q8Z2A5_SALTI | Q8Z2A5 from UniProtKB/TrEMBL  Length:193

    Alignment length:183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
         Q8Z2A5_SALTI     1 MQRCDWVSQDPLYIAYHDNEWGVPETDSRKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPIRIAAMQEEDVERLLQNTGIIRHRGKIQAIISNARAWLAMEQNGESFADFVWSFVDGQPQITQAASLDKIPTSTPASDALAKALKKRGFKFVGTTICYSFMQACGLVNDHITGCFCHP 183
               SCOP domains d2ofkb_ B: 3-Methyladenine DNA glycosylase I (Tag)                                                                                                                                      SCOP domains
               CATH domains 2ofkB00 B:1-183 Hypothetical protein; domain 2                                                                                                                                          CATH domains
           Pfam domains (1) -----Adenine_glyco-2ofkB01 B:6-183                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) -----Adenine_glyco-2ofkB02 B:6-183                                                                                                                                                      Pfam domains (2)
         Sec.struct. author .........hhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.....ee....hhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhh..ee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ofk B   1 MQRCDWVSQDPLYIAYHDNEWGVPETDSRKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPIRIAAMQEEDVERLLQNTGIIRHRGKIQAIISNARAWLAMEQNGESFADFVWSFVDGQPQITQAASLDKIPTSTPASDALAKALKKRGFKFVGTTICYSFMQACGLVNDHITGCFCHP 183
                                    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)
    → 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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Adenine_glyco] (4)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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(-) Related Entries Specified in the PDB File

2ofi TAG/DNA COMPLEX