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(-) Description

Title :  MUTY N-TERMINAL DOMAIN IN COMPLEX WITH UNDAMAGED DNA
 
Authors :  L. Wang, S. Chakravarthy, G. L. Verdine
Date :  27 Jun 16  (Deposition) - 08 Feb 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Adenine Glycosylase, Oxog, Dna Repair Protein, Lesion-Scanning Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Wang, S. Chakravarthy, G. L. Verdine
Structural Basis For The Lesion-Scanning Mechanism Of The Muty Dna Glycosylase.
J. Biol. Chem. V. 292 5007 2017
PubMed-ID: 28130451  |  Reference-DOI: 10.1074/JBC.M116.757039

(-) Compounds

Molecule 1 - ADENINE DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-229
    Gene: MUTY
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
 
Molecule 2 - DNA (5'-D(*AP*TP*CP*CP*TP*GP*TP*GP*CP*T)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:153 , CYS A:198 , CYS A:205 , CYS A:208 , CYS A:214 , ALA A:222binding site for residue SF4 A 301
2AC2SOFTWARESER A:118 , VAL A:123 , HOH A:415 , HOH A:499 , HOH A:507 , DA D:21binding site for residue CA A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KN8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:225 -Pro A:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KN8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KN8)

(-) Exons   (0, 0)

(no "Exon" information available for 5KN8)

(-) 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:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kn8 A   8 FPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVNGNVMRVLSRLFLVTDDIAKCSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKM 229
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227  


Chain C from PDB  Type:DNA  Length:10
                                          
                 5kn8 C   3 ATCCTGTGCT  12
                                    12


Chain D from PDB  Type:DNA  Length:10
                                          
                 5kn8 D  13 AGCACAGGAT  22
                                    22
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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  (0, 0)

(no "SCOP Domain" information available for 5KN8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KN8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KN8)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  5kn8
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  MUTY_GEOSE | P83847
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  3.2.2.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        MUTY_GEOSE | P83847: 1rrq 1rrs 1vrl 3fsp 3g0q 4yoq 4yph 4ypr 5dpk 5kn9

(-) Related Entries Specified in the PDB File

5kn9