3GV8

Human DNA polymerase iota in complex with T template DNA and incoming dGTP

• PDB DOI:  https://doi.org/10.2210/pdb3GV8/pdb
• NAKB: 3GV8

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


• Deposited: 2009-03-30 Released: 2009-06-02 
• Deposition Author(s): Kirouac, K.N., Ling, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

Literature

Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota

Kirouac, K.N., Ling, H.

(2009) EMBO J 28: 1644-1654

• PubMed: 19440206 
• DOI: https://doi.org/10.1038/emboj.2009.122
• Primary Citation of Related Structures:  
  3GV5, 3GV7, 3GV8


• PubMed Abstract: 
  

Human DNA polymerase iota (pol iota) is a unique member of Y-family polymerases, which preferentially misincorporates nucleotides opposite thymines (T) and halts replication at T bases. The structural basis of the high error rates remains elusive. We present three crystal structures of pol complexed with DNA containing a thymine base, paired with correct or incorrect incoming nucleotides. A narrowed active site supports a pyrimidine to pyrimidine mismatch and excludes Watson-Crick base pairing by pol. The template thymine remains in an anti conformation irrespective of incoming nucleotides. Incoming ddATP adopts a syn conformation with reduced base stacking, whereas incorrect dGTP and dTTP maintain anti conformations with normal base stacking. Further stabilization of dGTP by H-bonding with Gln59 of the finger domain explains the preferential T to G mismatch. A template 'U-turn' is stabilized by pol and the methyl group of the thymine template, revealing the structural basis of T stalling. Our structural and domain-swapping experiments indicate that the finger domain is responsible for pol's high error rates on pyrimidines and determines the incorporation specificity.

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Organizational Affiliation: 

Department of Biochemistry, University of Western Ontario, London, Ontario, Canada.

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: 52.44 kDa 
• Atom Count: 3,496 
• Modelled Residue Count: 390 
• Deposited Residue Count: 436 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase iota	A [auth B]	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: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*GP*GP*GP*TP*CP*CP*T)-3'	B [auth T]	9	N/A

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT	E [auth B]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
MG	D [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.07	α = 90
b = 98.07	β = 90
c = 203.38	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Kirouac, K.N., Ling, H.

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description