4K4H

Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)3TC-TP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for the binding and incorporation of nucleotide analogs with L-stereochemistry by human DNA polymerase lambda.

Vyas, R.Zahurancik, W.J.Suo, Z.

(2014) Proc.Natl.Acad.Sci.USA 111: E3033-E3042

  • DOI: 10.1073/pnas.1401286111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although lamivudine and emtricitabine, two L-deoxycytidine analogs, have been widely used as antiviral drugs for years, a structural basis for D-stereoselectivity against L-dNTPs, enantiomers of natural nucleotides (D-dNTPs), by any DNA polymerase or ...

    Although lamivudine and emtricitabine, two L-deoxycytidine analogs, have been widely used as antiviral drugs for years, a structural basis for D-stereoselectivity against L-dNTPs, enantiomers of natural nucleotides (D-dNTPs), by any DNA polymerase or reverse transcriptase has not been established due to lack of a ternary structure of a polymerase, DNA, and an incoming L-dNTP. Here, we report 2.10-2.25 Å ternary crystal structures of human DNA polymerase λ, DNA, and L-deoxycytidine 5'-triphosphate (L-dCTP), or the triphosphates of lamivudine ((-)3TC-TP) and emtricitabine ((-)FTC-TP) with four ternary complexes per asymmetric unit. The structures of these 12 ternary complexes reveal that relative to D-deoxycytidine 5'-triphosphate (D-dCTP) in the canonical ternary structure of Polλ-DNA-D-dCTP, L-dCTP, (-)3TC-TP, and (-)FTC-TP all have their ribose rotated by 180°. Among the four ternary complexes with a specific L-nucleotide, two are similar and show that the L-nucleotide forms three Watson-Crick hydrogen bonds with the templating nucleotide dG and adopts a chair-like triphosphate conformation. In the remaining two similar ternary complexes, the L-nucleotide surprisingly interacts with the side chain of a conserved active site residue R517 through one or two hydrogen bonds, whereas the templating dG is anchored by a hydrogen bond with the side chain of a semiconserved residue Y505. Furthermore, the triphosphate of the L-nucleotide adopts an unprecedented N-shaped conformation. Our mutagenic and kinetic studies further demonstrate that the side chain of R517 is critical for the formation of the abovementioned four complexes along proposed catalytic pathways for L-nucleotide incorporation and provide the structural basis for the D-stereoselectivity of a DNA polymerase.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase lambda
A, E, I, M
340Homo sapiensMutation(s): 0 
Gene Names: POLL
EC: 2.7.7.7, 4.2.99.-
Find proteins for Q9UGP5 (Homo sapiens)
Go to Gene View: POLL
Go to UniProtKB:  Q9UGP5
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3')B,F,J,N11Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')C,G,K,O6Homo sapiens
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*CP*G)-3')D,H,L,P4Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, F, I, M
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, E, F, I, J, M, N
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
1RZ
Query on 1RZ

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Download CCD File 
A, E, I, M
Lamivudine Triphosphate
Lamivudine-5'-triphosphate; 3TC Triphosphate; [[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
C8 H14 N3 O12 P3 S
YLEQMGZZMCJKCN-NKWVEPMBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 194.950α = 90.00
b = 97.440β = 90.00
c = 105.170γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-04-12 
  • Released Date: 2014-07-16 
  • Deposition Author(s): Vyas, R., Suo, Z.

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references
  • Version 1.2: 2014-08-13
    Type: Database references
  • Version 1.3: 2019-07-17
    Type: Data collection, Derived calculations, Structure summary