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(-) Description

Title :  MUTM CONTAINING F114A MUTATION BOUND TO OXOG-CONTAINING DNA
 
Authors :  R. J. Sung, M. Zhang, Y. Qi, G. L. Verdine
Date :  16 Jul 12  (Deposition) - 20 Feb 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Glycosylase, Dna Repair, Lesion Recognition, Base Extrusion, Disulfide Crosslinking, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Sung, M. Zhang, Y. Qi, G. L. Verdine
Structural And Biochemical Analysis Of Dna Helix Invasion B The Bacterial 8-Oxoguanine Dna Glycosylase Mutm.
J. Biol. Chem. V. 288 10012 2013
PubMed-ID: 23404556  |  Reference-DOI: 10.1074/JBC.M112.415612

(-) Compounds

Molecule 1 - FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: MUTM
    Gene: MUTM
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Synonym: FAPY-DNA GLYCOSYLASE, DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE MUTM
 
Molecule 2 - DNA (5'- D(P*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(8OG)P*AP*GP*(TX2) P*CP*TP*AP*CP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2TX21Mod. Nucleotide5'-O-{(R)-HYDROXY[(2-SULFANYLETHYL)AMINO]PHOSPHORYL}THYMIDINE
3ZN1Ligand/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 4G4R)

(-) 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 4G4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G4R)

(-) Exons   (0, 0)

(no "Exon" information available for 4G4R)

(-) 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    
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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
                                                                                                                                                                                                                                                                                            
               SCOP domains d4g4ra1 A:2-134 DNA repair protein MutM (Fpg)                                                                                        d4g4ra2 A:135-216 DNA repair protein MutM (Fpg)                                   d4g4ra3 A:238-274                     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...............hhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...................eeeee..eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g4r A   2 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKFLKFLLDRDALISHLRMEGRYAVASALEPLEPHTHVVFCFTDGSELRYRDVRKAGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    || 242       252       262       272  
                                                                                                                                                                                                                                                216|                                    
                                                                                                                                                                                                                                                 238                                    


Chain B from PDB  Type:DNA  Length:14
                                              
                 4g4r B   1 AGGTAGACTCGGAC  14
                                    10    


Chain C from PDB  Type:DNA  Length:12
                                            
                 4g4r C   4 GTCCgAGxCTAC  15
                                |  |13  
                                8-8OG   
                                  11-TX2
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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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G4R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G4R)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        P84131_GEOSE | P84131: 1l1t 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 3u6s 4g4n 4g4o 4g4q

(-) Related Entries Specified in the PDB File

4g4n 4g4o 4g4q