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(-) Description

Title :  STRUCTURE OF A THERMOSTABLE THYMINE-DNA GLYCOSYLASE
 
Authors :  C. D. Mol, A. S. Arvai, T. J. Begley, R. P. Cunningham, J. A. Tainer
Date :  14 Nov 01  (Deposition) - 23 Jan 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Dna Repair, Dna Glycosylase, Dna Mismatch, Methylation, Base Twisting, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. D. Mol, A. S. Arvai, T. J. Begley, R. P. Cunningham, J. A. Tainer
Structure And Activity Of A Thermostable Thymine-Dna Glycosylase: Evidence For Base Twisting To Remove Mismatche Normal Dna Bases.
J. Mol. Biol. V. 315 373 2002
PubMed-ID: 11786018  |  Reference-DOI: 10.1006/JMBI.2001.5264

(-) Compounds

Molecule 1 - POSSIBLE G-T MISMATCHES REPAIR ENZYME
    ChainsA
    EC Number3.2.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificMETHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid145262
    SynonymMISMATCH GLYCOSYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3SF41Ligand/IonIRON/SULFUR CLUSTER
4ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3SF41Ligand/IonIRON/SULFUR CLUSTER
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3SF42Ligand/IonIRON/SULFUR CLUSTER
4ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:31 , CYS A:66 , GLU A:68 , CL A:2001 , ACT A:3004BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREGLY A:124 , LYS A:125 , ACT A:3002 , HOH A:5063BINDING SITE FOR RESIDUE ACT A 3001
3AC3SOFTWARESER A:14 , TYR A:164 , ACT A:3001 , HOH A:5148 , HOH A:5186BINDING SITE FOR RESIDUE ACT A 3002
4AC4SOFTWAREGLN A:90 , LYS A:139 , GLY A:179 , HOH A:5133BINDING SITE FOR RESIDUE ACT A 3003
5AC5SOFTWAREGLU A:68 , ARG A:109 , ARG A:183 , ZN A:1001 , CL A:2001 , HOH A:5056 , HOH A:5191BINDING SITE FOR RESIDUE ACT A 3004
6AC6SOFTWARECYS A:66 , GLU A:68 , ZN A:1001 , ACT A:3004 , HOH A:5025BINDING SITE FOR RESIDUE CL A 2001
7AC7SOFTWAREARG A:33 , TYR A:36 , VAL A:110BINDING SITE FOR RESIDUE CL A 2002
8AC8SOFTWARECYS A:197 , CYS A:204 , CYS A:207 , MET A:209 , SER A:210 , CYS A:213 , TYR A:215BINDING SITE FOR RESIDUE SF4 A 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENDONUCLEASE_III_2PS01155 Endonuclease III family signature.GTMR_METTF108-137  1A:108-137
2ENDONUCLEASE_III_1PS00764 Endonuclease III iron-sulfur binding region signature.GTMR_METTF197-213  1A:197-213
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENDONUCLEASE_III_2PS01155 Endonuclease III family signature.GTMR_METTF108-137  1A:108-137
2ENDONUCLEASE_III_1PS00764 Endonuclease III iron-sulfur binding region signature.GTMR_METTF197-213  1A:197-213
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENDONUCLEASE_III_2PS01155 Endonuclease III family signature.GTMR_METTF108-137  2A:108-137
2ENDONUCLEASE_III_1PS00764 Endonuclease III iron-sulfur binding region signature.GTMR_METTF197-213  2A:197-213

(-) Exons   (0, 0)

(no "Exon" information available for 1KEA)

(-) 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:217
 aligned with GTMR_METTF | P29588 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:217
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       
           GTMR_METTF     3 DATNKKRKVFVSTILTFWNTDRRDFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFVKYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTCAAVMCLAFGKKAAMVDANFVRVINRYFGGSYENLNYNHKALWELAETLVPGGKCRDFNLGLMDFSAIICAPRKPKCEKCGMSKLCSYYEKC 219
               SCOP domains d1keaa_ A: Thymine-DNA glycosylase                                                                                                                                                                                        SCOP domains
               CATH domains 1keaA01                1keaA02 A:26-138 Hypothetical protein; domain 2                                                                  1keaA01 A:3-25,A:139-219                                                          CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------HHH-1keaA01 A:105-134         ------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------HhH-GPD-1keaA02 A:40-178                                                                                                                   ----------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------ENDONUCLEASE_III_2            -----------------------------------------------------------ENDONUCLEASE_III_------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kea A   3 DATNKKRKVFVSTILTFWNTDRRDFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFVKYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTCAAVMCLAFGKKAAMVDANFVRVINRYFGGSYENLNYNHKALWELAETLVPGGKCRDFNLGLMDFSAIICAPRKPKCEKCGMSKLCSYYEKC 219
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       

   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 Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HHH (112)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (GTMR_METTF | P29588)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003906    DNA-(apurinic or apyrimidinic site) lyase activity    Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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.
    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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