3TQ1

Human DNA Polymerase eta in binary complex with DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    3TQ1

  • 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, the na ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase eta A435Homo sapiensMutation(s): 0 
Gene Names: POLH, RAD30, RAD30A, XPV
EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens)
Explore Q9Y253 
Go to UniProtKB:  Q9Y253
NIH Common Fund Data Resources
PHAROS:  Q9Y253
GTEx:  ENSG00000170734
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')T13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      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: 2.56 Å
      • R-Value Free: 0.248 
      • R-Value Work: 0.186 
      • R-Value Observed: 0.191 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 98.914α = 90
      b = 98.914β = 90
      c = 81.185γ = 120
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHASERphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History 

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