Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 96507.63 
• Atom Count: 6331 
• Residue Count: 803 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1T3N

Structure of the catalytic core of DNA polymerase Iota in complex with DNA and dTTP

• DOI: 10.2210/pdb1T3N/pdb
• NDB: PD0543

• Classification: replication/DNA
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae


• Deposited: 2004-04-27 Released: 2004-07-20 
• Deposition Author(s): Nair, D.T., Johnson, R.E., Prakash, S., Prakash, L., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.286 
• R-Value Work: 0.265 

Literature

Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing.

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

(2004) Nature 430: 377-380

• PubMed: 15254543 
• DOI: 10.1038/nature02692
• Also Cited By: 1ZET


• PubMed Abstract: 
  

Almost all DNA polymerases show a strong preference for incorporating the nucleotide that forms the correct Watson-Crick base pair with the template base. In addition, the catalytic efficiencies with which any given polymerase forms the four possible correct base pairs are roughly the same. Human DNA polymerase-iota (hPoliota), a member of the Y family of DNA polymerases, is an exception to these rules. hPoliota incorporates the correct nucleotide opposite a template adenine with a several hundred to several thousand fold greater efficiency than it incorporates the correct nucleotide opposite a template thymine, whereas its efficiency for correct nucleotide incorporation opposite a template guanine or cytosine is intermediate between these two extremes. Here we present the crystal structure of hPoliota bound to a template primer and an incoming nucleotide. The structure reveals a polymerase that is 'specialized' for Hoogsteen base-pairing, whereby the templating base is driven to the syn conformation. Hoogsteen base-pairing offers a basis for the varied efficiencies and fidelities of hPoliota opposite different template bases, and it provides an elegant mechanism for promoting replication through minor-groove purine adducts that interfere with replication.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
polymerase (DNA directed) iota	A, B	388	Homo sapiens	Mutation(s): 0  Gene Names: POLI (RAD30B) EC: 2.7.7.7
Find proteins for Q9UNA4 (Homo sapiens) Go to Gene View: POLI Go to UniProtKB:  Q9UNA4

Entity ID: 1
Molecule	Chains	Length	Organism
Template DNA strand	T	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
Primer DNA strand	P	13	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TTP	B	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
MG	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DOC	P	DNA LINKING	C9 H14 N3 O6 P		DC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.286 
• R-Value Work: 0.265 
• Space Group: P 6₅

Unit Cell:

Length (Å)	Angle (°)
a = 98.831	α = 90.00
b = 98.831	β = 90.00
c = 202.755	γ = 120.00

Software Package:

Software Name	Purpose
CNS	refinement
SOLVE	phasing
SCALEPACK	data scaling
HKL-2000	data reduction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-27 
• Released Date: 2004-07-20 
• Deposition Author(s): Nair, D.T., Johnson, R.E., Prakash, S., Prakash, L., Aggarwal, A.K.

Revision History 

• Version 1.0: 2004-07-20
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2015-09-09
  Type: Other
• Version 1.4: 2018-04-18
  Type: Data collection, Derived calculations