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(-) Description

Title :  ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING AN ABASIC SITE AND A FREE NUCLEOBASE (100% PRODUCT AT 240 HOURS)
 
Authors :  E. A. Mullins, B. F. Eichman
Date :  16 Jul 15  (Deposition) - 28 Oct 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Glycosylase, Heat-Like Repeat, Protein-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. A. Mullins, R. Shi, Z. D. Parsons, P. K. Yuen, S. S. David, Y. Igarashi B. F. Eichman
The Dna Glycosylase Alkd Uses A Non-Base-Flipping Mechanism To Excise Bulky Lesions.
Nature V. 527 254 2015
PubMed-ID: 26524531  |  Reference-DOI: 10.1038/NATURE15728

(-) Compounds

Molecule 1 - ALKD
    Atcc14579
    ChainsA
    EC Number3.2.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBG103
    Expression System StrainHMS174
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneIKE_03968
    Organism ScientificBACILLUS CEREUS
    Organism Taxid1396
 
Molecule 2 - DNA (5'-D(*CP*CP*CP*GP*AP*(ORP)P*AP*GP*TP*CP*CP*G)-3')
    ChainsB
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3')
    ChainsC
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    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
154K1Ligand/Ion7-METHYL-3H-IMIDAZO[4,5-C]PYRIDIN-4-AMINE
2ORP1Mod. Nucleotide2-DEOXY-5-PHOSPHONO-RIBOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:27 , DA B:5 , DA B:7 , HOH B:208 , HOH B:209 , DT C:18 , DT C:19 , DT C:20binding site for residue 54K B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CL9)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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
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Chain A from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cl9 A  -1 VPMHPFVKALQEHFTAHQNPEKAEPMARYMKNHFLFLGIQTPERRQLLKDIIQIHTLPDQKDFQIIIRELWDLPEREFQAAALDIMQKYKKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFLKHPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWIIGQLHSSKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNELAPLSKREAIKHIKQNYGINN 229
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228 

Chain B from PDB  Type:DNA  Length:12
                                            
                 5cl9 B   1 CCCGAxAGTCCG  12
                                 |  10  
                                 6-ORP  

Chain C from PDB  Type:DNA  Length:12
                                            
                 5cl9 C  13 CGGACTTTCGGG  24
                                    22  

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5CL9)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

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

UniProtKB/Swiss-Prot
        R8GWR7_BACCE | R8GWR75cl3 5cl4 5cl5 5cl6 5cl7 5cl8 5cla 5clb 5clc 5cld 5cle
UniProtKB/TrEMBL
        Q816E8_BACCR | Q816E83bvs 3jx7 3jxy 3jxz 3jy1 5cl3 5cl4 5cl5 5cl6 5cl7 5cl8 5cla 5clb 5clc 5cld 5cle 5kub

(-) Related Entries Specified in the PDB File

5cl3 5cl4 5cl5 5cl6 5cl7 5cl8 5cla 5clb 5clc 5cld 5cle