3PZP

Human DNA polymerase kappa extending opposite a cis-syn thymine dimer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.336 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Role of human DNA polymerase kappa in extension opposite from a cis-syn thymine dimer.

Vasquez-Del Carpio, R., Silverstein, T.D., Lone, S., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2011) J.Mol.Biol. 408: 252-261

  • DOI: 10.1016/j.jmb.2011.02.042

  • PubMed Abstract: 

    • Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase κ (Polκ), a member of the Y-fa ...

    Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase κ (Polκ), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Polκ in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Polκ in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.

    Organizational Affiliation: 

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase kappa
A, B
517Homo sapiensMutation(s): 0 
Gene Names: POLK (DINB1)
EC: 2.7.7.7
Find proteins for Q9UBT6 (Homo sapiens)
Go to Gene View: POLK
Go to UniProtKB:  Q9UBT6
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3'P,Q13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'T,U17N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP
Download SDF File 
Download CCD File 
A, B
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TTD
Query on TTD
T, U
DNA LINKINGC20 H28 N4 O15 P2DT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.336 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 117.136α = 90.00
b = 154.476β = 90.00
c = 217.854γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release