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(-) Description

Title :  MUTY ADENINE GLYCOSYLASE BOUND TO A TRANSITION STATE ANALOG (1N) PAIRED WITH D(8-OXOG) IN DUPLEXED DNA TO 2.2 A
 
Authors :  M. P. Horvath, V. L. O'Shea, S. Cao, S. S. David
Date :  12 Sep 15  (Deposition) - 23 Sep 15  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Dna Repair, Glycosylase, Transition State Analog, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. D. Woods, V. L. O'Shea, A. Chu, S. Cao, J. L. Richards, M. P. Horvath, S. S. David
Structure And Stereochemistry Of The Base Excision Repair Glycosylase Muty Reveal A Mechanism Similar To Retaining Glycosidases.
Nucleic Acids Res. V. 44 801 2016
PubMed-ID: 26673696  |  Reference-DOI: 10.1093/NAR/GKV1469

(-) Compounds

Molecule 1 - A/G-SPECIFIC ADENINE GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MUTY
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
 
Molecule 2 - DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3NR11Mod. Nucleotide(3R,4R)-3-HYDROXY-4-[(PHOSPHONOOXY)METHYL]PYRROLIDINIUM
4SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:198 , CYS A:205 , CYS A:208 , GLN A:211 , CYS A:214binding site for residue SF4 A 401
2AC2SOFTWARESER A:118 , VAL A:123 , HOH A:509 , HOH A:529 , HOH C:102binding site for residue CA A 402
3AC3SOFTWAREASP A:257 , THR A:259binding site for residue CA A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:225 -Pro A:226
2Asp A:274 -Gly A:275
3Glu A:329 -Pro A:330

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DPK)

(-) 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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhhh.......hhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh.........eeeeeeeeeee.....eeeee..........ee..eee....hhhhhhhhhhhhh......eeeeee...eeeeeeeeeee..........eeeehhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dpk A   7 RFPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVDGNVMRVLSRLFLVTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRKRDSTGLLANLWEFPSCETDGADGKEKLEQMVGEQELTEPIVSFEHAFSHLVWQLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVWREYKEWAS 360
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  ||   301       311       321       331       341       351         
                                                                                                                                                                                                                                                                                                                    289|                                                                 
                                                                                                                                                                                                                                                                                                                     295                                                                 


Chain B from PDB  Type:DNA  Length:11
                                           
                 5dpk B   1 AAGACxTGGAC  11
                                 |  10 
                                 6-8OG 


Chain C from PDB  Type:DNA  Length:10
                                          
                 5dpk C  13 GTCCAxGTCT  22
                                 |  22
                                18-NR1
   Legend:   → Mismatch (orange background)
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    → 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 5DPK)

(-) CATH Domains  (0, 0 ; only for superseded entry 3FSQ: 3,3)

(no "CATH Domain" information available for 5DPK, only for superseded entry 3FSQ replaced by 5DPK)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:274 - Gly A:275   [ RasMol ]  
    Glu A:329 - Pro A:330   [ RasMol ]  
    Leu A:225 - Pro A:226   [ RasMol ]  
 

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  MUTY_GEOSE | P83847
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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 5kn8 5kn9

(-) Related Entries Specified in the PDB File

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