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(-) Description

Title :  BENZYLATED HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE
 
Authors :  D. S. Daniels, J. A. Tainer
Date :  18 Feb 00  (Deposition) - 12 Apr 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Alkyltransferase, Methyltransferase, Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. S. Daniels, C. D. Mol, A. S. Arvai, S. Kanugula, A. E. Pegg, J. A. Tainer
Active And Alkylated Human Agt Structures: A Novel Zinc Site, Inhibitor And Extrahelical Base Binding.
Embo J. V. 19 1719 2000
PubMed-ID: 10747039  |  Reference-DOI: 10.1093/EMBOJ/19.7.1719
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE
    ChainsA
    EC Number2.1.1.63
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCYS 145 HAS BEEN ALKYLATED BY REACTION WITH O6-BENZYLGUANINE
    SynonymAGT, O6-METHYLGUANINE-DNA METHYLTRANSFERASE, MGMT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BCS1Mod. Amino AcidBENZYLCYSTEINE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:5 , CYS A:24 , HIS A:29 , HIS A:85BINDING SITE FOR RESIDUE ZN A 208
2ACTAUTHORBCS A:145ACTIVE SITE CYSTEINE, BENZYLATED

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EH8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:55 -Pro A:56

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (10, 10)

Asymmetric/Biological Unit (10, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_014750E30KMGMT_HUMANPolymorphism2020893AE30K
02UniProtVAR_056129L53FMGMT_HUMANPolymorphism12917AL53F
03UniProtVAR_029112P58SMGMT_HUMANPolymorphism2308322AP58S
04UniProtVAR_020354W65CMGMT_HUMANPolymorphism2282164AW65C
05UniProtVAR_014751L84FMGMT_HUMANPolymorphism12917AL84F
06UniProtVAR_056130I112VMGMT_HUMANPolymorphism2308321AI112V
07UniProtVAR_014752I143VMGMT_HUMANPolymorphism2308321AI143V
08UniProtVAR_014753G160RMGMT_HUMANPolymorphism2308318AG160R
09UniProtVAR_014754E166DMGMT_HUMANPolymorphism2308320AE166D
10UniProtVAR_014755K178RMGMT_HUMANPolymorphism2308327AK178R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MGMTPS00374 Methylated-DNA--protein-cysteine methyltransferase active site.MGMT_HUMAN143-149  1A:143-149

(-) Exons   (0, 0)

(no "Exon" information available for 1EH8)

(-) 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:166
 aligned with MGMT_HUMAN | P16455 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:175
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174     
           MGMT_HUMAN     5 CEMKRTTLDSPLGKLELSGCEQGLHEIKLLGKGTSAADAVEVPAPAAVLGGPEPLMQCTAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYQQLAALAGNPKAARAVGGAMRGNPVPILIPCHRVVCSSGAVGNYSGGLAVKEWLLAHEGHRLGKP 179
               SCOP domains d1eh8a2 A:5-91 O6-alkylguanine-         DNA alkyltransferase                           d1eh8a1 A:92-179 O6-alkylguanine-DNA alkyltransferase                                    SCOP domains
               CATH domains -1eh8A01 A:6-85 O6-alkylguanine         -DNA Alkyltransferase; Chain A, domain 1 1eh8A02 A:86-175 'winged helix' repressor DNA binding domain                              ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..eeeeeeee..eeeeeeeee---------...........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhhh.....eehhhhhhhh....hhhhhhhhhhh...........ee...........hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------K----------------------F----S------C------------------F---------------------------V------------------------------V----------------R-----D-----------R- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------MGMT   ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eh8 A   5 CEMKRTTLDSPLGKLELSGCEQGLHEIKLLG---------EVPAPAAVLGGPEPLMQCTAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYQQLAALAGNPKAARAVGGAMRGNPVPILIPcHRVVCSSGAVGNYSGGLAVKEWLLAHEGHRLGKP 179
                                    14        24        34|        -|       54        64        74        84        94       104       114       124       134       144|      154       164       174     
                                                         35        45                                                                                                 145-BCS                              

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EH8)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MGMT_HUMAN | P16455)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009008    DNA-methyltransferase activity    Catalysis of the transfer of a methyl group to a DNA molecule.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006266    DNA ligation    The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    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:0071479    cellular response to ionizing radiation    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 ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
    GO:0071407    cellular response to organic cyclic compound    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 an organic cyclic compound stimulus.
    GO:0034599    cellular response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0060644    mammary gland epithelial cell differentiation    The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0045739    positive regulation of DNA repair    Any process that activates or increases the frequency, rate or extent of DNA repair.
    GO:2000781    positive regulation of double-strand break repair    Any process that activates or increases the frequency, rate or extent of double-strand break repair.
    GO:0043281    regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that modulates the activity of a cysteine-type endopeptidase involved in apoptosis.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0045471    response to ethanol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0051593    response to folic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a folic acid stimulus.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MGMT_HUMAN | P164551eh6 1eh7 1qnt 1t38 1t39 1yfh

(-) Related Entries Specified in the PDB File

1eh6 1EH6 CONTAINS THE NATIVE PROTEIN
1eh7 1EH7 CONTAINS THE METHYLATED PRODUCT