2DPJ

structure of hPoli with DNA and dTTP

• PDB DOI:  https://doi.org/10.2210/pdb2DPJ/pdb
• NAKB: 2DPJ

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2006-05-12 Released: 2006-07-04 
• Deposition Author(s): Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 

Literature

Hoogsteen base pair formation promotes synthesis opposite the 1,N(6)-ethenodeoxyadenosine lesion by human DNA polymerase iota.

Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2006) Nat Struct Mol Biol 13: 619-625

• PubMed: 16819516 
• DOI: https://doi.org/10.1038/nsmb1118
• Primary Citation of Related Structures:  
  2DPI, 2DPJ


• PubMed Abstract: 
  

The 1,N6-ethenodeoxyadenosine (epsilon dA) lesion is promutagenic and has been implicated in carcinogenesis. We show here that human Pol iota, a Y-family DNA polymerase, can promote replication through this lesion by proficiently incorporating a nucleotide opposite it. The structural basis of this action is rotation of the epsilon dA adduct to the syn conformation in the Pol iota active site and presentation of its 'Hoogsteen edge' for hydrogen-bonding with incoming dTTP or dCTP. We also show that Pol zeta carries out the subsequent extension reaction and that efficiency of extension from epsilon dA x T is notably higher than from epsilon dA x C. Together, our studies reveal for the first time how the exocyclic epsilon dA adduct is accommodated in a DNA polymerase active site, and they show that the combined action of Pol iota and Pol zeta provides for efficient and error-free synthesis through this potentially carcinogenic DNA lesion.

---

Organizational Affiliation: 

Department of Molecular Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, New York 10029, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.42 kDa 
• Atom Count: 3,357 
• Modelled Residue Count: 389 
• Deposited Residue Count: 436 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase iota	C [auth A]	420	Homo sapiens	Mutation(s): 0  Gene Names: POLI, RAD30B EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNA4 (Homo sapiens) Explore Q9UNA4  Go to UniProtKB:  Q9UNA4
PHAROS:  Q9UNA4

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'	A [auth P]	7	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3'	B [auth T]	9	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	F [auth A]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.059	α = 90
b = 98.059	β = 90
c = 203.102	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance