4YP3

Mutant Human DNA Polymerase Eta Q38A/R61A Inserting dCTP Opposite an 8-Oxoguanine Lesion

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase eta in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine.

Su, Y., Patra, A., Harp, J.M., Egli, M., Guengerich, F.P.

(2015) J Biol Chem 290: 15921-15933

  • DOI: 10.1074/jbc.M115.653691
  • Primary Citation of Related Structures:  
    4YP3, 4YQW, 4YR0, 4YR2, 4YR3

  • PubMed Abstract: 

    • Like the other Y-family DNA polymerases, human DNA polymerase η (hpol η) has relatively low fidelity and is able to tolerate damage during DNA synthesis, including 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxoG), one of the most abundant DNA lesions in the genome ...

    Like the other Y-family DNA polymerases, human DNA polymerase η (hpol η) has relatively low fidelity and is able to tolerate damage during DNA synthesis, including 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxoG), one of the most abundant DNA lesions in the genome. Crystal structures show that Arg-61 and Gln-38 are located near the active site and may play important roles in the fidelity and efficiency of hpol η. Site-directed mutagenesis was used to replace these side chains either alone or together, and the wild type or mutant proteins were purified and tested by replicating DNA past deoxyguanosine (G) or 8-oxoG. The catalytic activity of hpol η was dramatically disrupted by the R61M and Q38A/R61A mutations, as opposed to the R61A and Q38A single mutants. Crystal structures of hpol η mutant ternary complexes reveal that polarized water molecules can mimic and partially compensate for the missing side chains of Arg-61 and Gln-38 in the Q38A/R61A mutant. The combined data indicate that the positioning and positive charge of Arg-61 synergistically contribute to the nucleotidyl transfer reaction, with additional influence exerted by Gln-38. In addition, gel filtration chromatography separated multimeric and monomeric forms of wild type and mutant hpol η, indicating the possibility that hpol η forms multimers in vivo.

    Organizational Affiliation: 

    From the Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146 f.guengerich@vanderbilt.edu.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase eta A435Homo sapiensMutation(s): 2 
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
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3')T12synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')P8synthetic construct
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DCP
      Query on DCP
      Download Ideal Coordinates CCD File 
      A
      		2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
      C9 H16 N3 O13 P3
      RGWHQCVHVJXOKC-SHYZEUOFSA-N      		 Ligand Interaction
      GOL
      Query on GOL
      Download Ideal Coordinates CCD File 
      A
      		GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N      		 Ligand Interaction
      CA
      Query on CA
      Download Ideal Coordinates CCD File 
      A
      		CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.89 Å
      • R-Value Free: 0.215 
      • R-Value Work: 0.169 
      • R-Value Observed: 0.171 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 98.769α = 90
      b = 98.769β = 90
      c = 81.966γ = 120
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      ARPmodel building
      PHASERphasing
      HKL-2000data scaling
      Cootmodel building
      HKL-2000data reduction

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History & Funding Information

      Deposition Data

      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesR01 ES010375
      National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01 CA160032

      Revision History  (Full details and data files)

      • Version 1.0: 2015-05-13
        Type: Initial release
      • Version 1.1: 2015-05-20
        Changes: Database references
      • Version 1.2: 2015-07-08
        Changes: Database references
      • Version 1.3: 2017-09-20
        Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Source and taxonomy, Structure summary
      • Version 1.4: 2019-12-04
        Changes: Author supporting evidence