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(-) Description

Title :  MUTM SET 1 TPG
 
Authors :  R. J. Sung, M. Zhang, Y. Qi, G. L. Verdine
Date :  12 Oct 11  (Deposition) - 25 Apr 12  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Glycosylase, Dna Repair, Sequence Context, Lesion Recognition, Disulfide Crosslinking, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. J. Sung, M. Zhang, Y. Qi, G. L. Verdine
Sequence-Dependent Structural Variation In Dna Undergoing Intrahelical Inspection By The Dna Glycosylase Mutm.
J. Biol. Chem. V. 287 18044 2012
PubMed-ID: 22465958  |  Reference-DOI: 10.1074/JBC.M111.313635

(-) Compounds

Molecule 1 - FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE
    ChainsA
    EC Number3.2.2.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
 
Molecule 2 - DNA (5'-D(*A*GP*GP*TP*AP*GP*AP*TP*CP*CP*AP*GP*AP*CP*GP*C)- 3')
    ChainsB
    EngineeredYES
    Other DetailsSYNTHETIC DNA
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*TP*GP*CP*GP*TP*CP*TP*GP*GP*AP*(08Q) P*CP*TP*AP*CP*C)-3')
    ChainsC
    EngineeredYES
    Other DetailsSYNTHETIC DNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
108Q1Mod. Nucleotide5'-O-{(S)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE
2ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:249 , CYS A:252 , CYS A:269 , CYS A:272BINDING SITE FOR RESIDUE ZN A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U6S)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:36 -Pro A:37
2Pro A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U6S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U6S)

(-) Exons   (0, 0)

(no "Exon" information available for 3U6S)

(-) 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:252
 aligned with P84131_GEOSE | P84131 from UniProtKB/TrEMBL  Length:274

    Alignment length:273
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   
         P84131_GEOSE     2 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKFLKFLLDRDALISHLRMEGRYAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDQTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTVRTYVNTQGEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 274
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeeee.hhh.eee..hhhhhhhhhh.....eeeee..eeeee...eeeeee.....eeeeee........eeeeeee...eeeeee......eeeeee.hhhhhh...............hhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh---------------------...................eeeee..eeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u6s A   2 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKFLKFLLDRDALISHLRMEGRYAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVM---------------------HLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    |    -         -      |241       251       261       271   
                                                                                                                                                                                                                                                216                   238                                    

Chain B from PDB  Type:DNA  Length:13
                                             
                 3u6s B   2 GGTAGATCCAGAC  14
                                    11   

Chain C from PDB  Type:DNA  Length:12
                                            
                 3u6s C   4 GTCTGGAxCTAC  15
                                   |13  
                                  11-08Q

   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  (0, 0)

(no "SCOP Domain" information available for 3U6S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U6S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U6S)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P84131_GEOSE | P84131)
molecular function
    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:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    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:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008534    oxidized purine nucleobase lesion DNA N-glycosylase activity    Catalysis of the removal of oxidized purine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar. The reaction involves the formation of a covalent enzyme-substrate intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apurinic (AP) site.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).

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 Related Entries

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

UniProtKB/TrEMBL
        P84131_GEOSE | P841311l1t 1l1z 1l2b 1l2c 1r2y 1r2z 2f5n 2f5o 2f5p 2f5q 2f5s 3go8 3gp1 3gpp 3gpu 3gpx 3gpy 3gq3 3gq4 3gq5 3jr4 3jr5 3sar 3sas 3sat 3sau 3sav 3saw 3sbj 3u6c 3u6d 3u6e 3u6l 3u6m 3u6o 3u6p 3u6q 4g4n 4g4o 4g4q 4g4r

(-) Related Entries Specified in the PDB File

3u6c 3u6d 3u6e 3u6l 3u6m 3u6o 3u6p 3u6q