3TQ1

Human DNA Polymerase eta in binary complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.556 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Human DNA Polymerase Eta Is Pre-Aligned for dNTP Binding and Catalysis.

Ummat, A.Silverstein, T.D.Jain, R.Buku, A.Johnson, R.E.Prakash, L.Prakash, S.Aggarwal, A.K.

(2012) J.Mol.Biol. 415: 627-634

  • DOI: 10.1016/j.jmb.2011.11.038

  • PubMed Abstract: 
  • Pre-steady-state kinetic studies on Y-family DNA polymerase η (Polη) have suggested that the polymerase undergoes a rate-limiting conformational change step before the phosphoryl transfer of the incoming nucleotide to the primer terminus. However, th ...

    Pre-steady-state kinetic studies on Y-family DNA polymerase η (Polη) have suggested that the polymerase undergoes a rate-limiting conformational change step before the phosphoryl transfer of the incoming nucleotide to the primer terminus. However, the nature of this rate-limiting conformational change step has been unclear, due in part to the lack of structural information on the Polη binary complex. We present here for the first time a crystal structure of human Polη (hPolη) in binary complex with its DNA substrate. We show that the hPolη domains move only slightly on dNTP binding and that the polymerase by and large is pre-aligned for dNTP binding and catalysis. We also show that there is no major reorientation of the DNA from a nonproductive to a productive configuration and that the active site is devoid of metals in the absence of dNTP. Together, these observations lead us to suggest that the rate-limiting conformational change step in the Polη replication cycle likely corresponds to a rate-limiting entry of catalytic metals in the active site.


    Organizational Affiliation

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase eta
A
435Homo sapiensMutation(s): 0 
Gene Names: POLH (RAD30, RAD30A, XPV)
EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens)
Go to Gene View: POLH
Go to UniProtKB:  Q9Y253
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')T13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')P9N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.556 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.186 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 98.914α = 90.00
b = 98.914β = 90.00
c = 81.185γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release