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(-) Description

Title :  CRYSTAL STRUCTURE OF O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS KODAKARAENSIS STRAIN KOD1
 
Authors :  H. Hashimoto, T. Inoue, M. Nishioka, S. Fujiwara, M. Takagi, T. Imanaka
Date :  12 Jan 99  (Deposition) - 07 Jan 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Methyltransferase, Dna Repair Protein, Suicidal Enzyme, Hyperthermostability, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Hashimoto, T. Inoue, M. Nishioka, S. Fujiwara, M. Takagi, T. Imanaka, Y. Kai
Hyperthermostable Protein Structure Maintained By Intra And Inter-Helix Ion-Pairs In Archaeal O6-Methylguanine-Dna Methyltransferase.
J. Mol. Biol. V. 292 707 1999
PubMed-ID: 10497033  |  Reference-DOI: 10.1006/JMBI.1999.3100
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (O6-METHYLGUANINE-DNA METHYLTRANSFERASE)
    ChainsA
    EC Number2.1.1.63
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificTHERMOCOCCUS KODAKARENSIS
    Organism Taxid69014
    StrainKOD1
    SynonymMGMT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8 , THR A:111 , TYR A:112 , GLY A:113 , ALA A:146 , HIS A:147 , HOH A:539 , HOH A:540 , HOH A:600BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARELYS A:6 , ARG A:8 , ARG A:124 , HOH A:547 , HOH A:621BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREHIS A:46 , ARG A:50 , ASN A:120 , ARG A:132BINDING SITE FOR RESIDUE SO4 A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MGMTPS00374 Methylated-DNA--protein-cysteine methyltransferase active site.OGT_THEKO139-145  1A:139-145

(-) Exons   (0, 0)

(no "Exon" information available for 1MGT)

(-) 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:169
 aligned with OGT_THEKO | O74023 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         
            OGT_THEKO     1 MLSVEKFRVGERVVWIGVIFSGRVQGIAFAFDRGTLMKRIHDLAEHLGKRGVSISLDVQPSDYPEKVFKVLIGELDNASFLRELSFEGVTPFEKKVYEWLTKNVKRGSVITYGDLAKALNTSPRAVGGAMKRNPYPIVVPCHRVVAHDGIGYYSSGIEEKKFLLEIEGV 169
               SCOP domains d1mgta2 A:1-88 O6-alkylguanine-DNA alkyltransferase                                     d1mgta1 A:89-169 O6-alkylguanine-DNA alkyltransferase                             SCOP domains
               CATH domains 1mgtA01 A:1-88  [code=3.30.160.70, no name defined]                                     1mgtA02 A:89-169 'winged helix' repressor DNA binding domain                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeeeee.eeeeeeee..hhhhhhhhhhhhhhhhhh............hhhhhhhhh.....hhhhhhh.......hhhhhhhhhhhhh........hhhhhhh....hhhhhhhhh.........hhh.............hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------MGMT   ------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mgt A   1 MLSVEKFRVGERVVWIGVIFSGRVQGIAFAFDRGTLMKRIHDLAEHLGKRGVSISLDVQPSDYPEKVFKVLIGELDNASFLRELSFEGVTPFEKKVYEWLTKNVKRGSVITYGDLAKALNTSPRAVGGAMKRNPYPIVVPCHRVVAHDGIGYYSSGIEEKKFLLEIEGV 169
                                    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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1MGT)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OGT_THEKO | O74023)
molecular function
    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:0003908    methylated-DNA-[protein]-cysteine S-methyltransferase activity    Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006307    DNA dealkylation involved in DNA repair    The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
    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: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.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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