5VHV

Pseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to DNA containing an oxocarbenium-intermediate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.799 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC.

Shi, R.Mullins, E.A.Shen, X.X.Lay, K.T.Yuen, P.K.David, S.S.Rokas, A.Eichman, B.F.

(2018) EMBO J. 37: 63-74

  • DOI: 10.15252/embj.201797833
  • Primary Citation of Related Structures:  5VI0

  • PubMed Abstract: 
  • DNA glycosylases preserve genome integrity and define the specificity of the base excision repair pathway for discreet, detrimental modifications, and thus, the mechanisms by which glycosylases locate DNA damage are of particular interest. Bacterial ...

    DNA glycosylases preserve genome integrity and define the specificity of the base excision repair pathway for discreet, detrimental modifications, and thus, the mechanisms by which glycosylases locate DNA damage are of particular interest. Bacterial AlkC and AlkD are specific for cationic alkylated nucleobases and have a distinctive HEAT-like repeat (HLR) fold. AlkD uses a unique non-base-flipping mechanism that enables excision of bulky lesions more commonly associated with nucleotide excision repair. In contrast, AlkC has a much narrower specificity for small lesions, principally N3-methyladenine (3mA). Here, we describe how AlkC selects for and excises 3mA using a non-base-flipping strategy distinct from that of AlkD. A crystal structure resembling a catalytic intermediate complex shows how AlkC uses unique HLR and immunoglobulin-like domains to induce a sharp kink in the DNA, exposing the damaged nucleobase to active site residues that project into the DNA This active site can accommodate and excise N3-methylcytosine (3mC) and N1-methyladenine (1mA), which are also repaired by AlkB-catalyzed oxidative demethylation, providing a potential alternative mechanism for repair of these lesions in bacteria.


    Organizational Affiliation

    Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alkylpurine DNA glycosylase AlkC
A, B
361N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3')C,E11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')D,F11synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
C, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
9B4
Query on 9B4

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Download CCD File 
D, F
(2R,5R,13R,16R)-9-(hydroxymethyl)-9-{[(2R)-2-hydroxypropoxy]methyl}-5,13-dimethyl-4,7,11,14-tetraoxaheptadecane-2,16-diol
Pentaerythritol propoxylate (5/4 PO/OH)
C20 H42 O9
XAZUABIGWFVOAV-FVVUREQNSA-N
 Ligand Interaction
MES
Query on MES

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A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NRI
Query on NRI
C, E
DNA LINKINGC5 H12 N O5 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.799 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.141 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 198.373α = 90.00
b = 198.373β = 90.00
c = 60.189γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-04-13 
  • Released Date: 2017-10-25 
  • Deposition Author(s): Shi, R., Eichman, B.F.

Funding OrganizationCountryGrant Number
National Science Foundation (United States)United States1517695

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Database references