5EWE | pdb_00005ewe

Ternary complex of human DNA polymerase eta inserting rCTP opposite template G

• PDB DOI: https://doi.org/10.2210/pdb5EWE/pdb
• NAKB: 5EWE

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2015-11-20 Released: 2016-01-13 
• Deposition Author(s): Su, Y., Egli, M., Guengerich, F.P.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase eta.

Su, Y., Egli, M., Guengerich, F.P.

(2016) J Biological Chem 291: 3747-3756

• PubMed: 26740629 
• DOI: https://doi.org/10.1074/jbc.M115.706226
• Primary Citation Related Structures: 
  5EWE, 5EWF, 5EWG


• PubMed Abstract: 
  

  Ribonucleotides and 2'-deoxyribonucleotides are the basic units for RNA and DNA, respectively, and the only difference is the extra 2'-OH group on the ribonucleotide sugar. Cellular rNTP concentrations are much higher than those of dNTP. When copying DNA, DNA polymerases not only select the base of the incoming dNTP to form a Watson-Crick pair with the template base but also distinguish the sugar moiety. Some DNA polymerases use a steric gate residue to prevent rNTP incorporation by creating a clash with the 2'-OH group. Y-family human DNA polymerase η (hpol η) is of interest because of its spacious active site (especially in the major groove) and tolerance of DNA lesions. Here, we show that hpol η maintains base selectivity when incorporating rNTPs opposite undamaged DNA and the DNA lesions 7,8-dihydro-8-oxo-2'-deoxyguanosine and cyclobutane pyrimidine dimer but with rates that are 10(3)-fold lower than for inserting the corresponding dNTPs. X-ray crystal structures show that the hpol η scaffolds the incoming rNTP to pair with the template base (dG) or 7,8-dihydro-8-oxo-2'-deoxyguanosine with a significant propeller twist. As a result, the 2'-OH group avoids a clash with the steric gate, Phe-18, but the distance between primer end and Pα of the incoming rNTP increases by 1 Å, elevating the energy barrier and slowing polymerization compared with dNTP. In addition, Tyr-92 was identified as a second line of defense to maintain the position of Phe-18. This is the first crystal structure of a DNA polymerase with an incoming rNTP opposite a DNA lesion.

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Organizational Affiliation: 
• From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146 [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.45 kDa 
• Atom Count: 4,272 
• Modeled Residue Count: 447 
• Deposited Residue Count: 455 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase eta	A	435	Homo sapiens	Mutation(s): 0  Gene Names: POLH, RAD30, RAD30A, XPV EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y253 (Homo sapiens) Explore Q9Y253  Go to UniProtKB:  Q9Y253
PHAROS:  Q9Y253 GTEx:  ENSG00000170734

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*TP*GP*AP*TP*GP*AP*CP*GP*CP*T)-3')	B [auth T]	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')	C [auth P]	8	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTP	D [auth A]	CYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-XVFCMESISA-N
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.282	α = 90
b = 99.282	β = 90
c = 81.895	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
ARP	model building
Coot	model building
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Su, Y., Egli, M., Guengerich, F.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	R01 ES010375
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA160032

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-01-20
  Changes: Database references
• Version 1.2: 2016-03-02
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description