Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52474.94 
• Atom Count: 3135 
• Residue Count: 438 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2FLP

Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G)

• DOI: 10.2210/pdb2FLP/pdb
• NDB: PD0779

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


• Deposited: 2006-01-06 Released: 2006-12-05 
• Deposition Author(s): Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.276 
• R-Value Work: 0.228 

Literature

An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site.

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

(2006) Structure 14: 749-755

• PubMed: 16615915 
• DOI: 10.1016/j.str.2006.01.010
• Primary Citation of Related Structures:  
  2FLN, 2FLL


• PubMed Abstract: 
  

Substrate-induced conformational change of the protein is the linchpin of enzymatic reactions. Replicative DNA polymerases, for example, convert from an open to a closed conformation in response to dNTP binding. Human DNA polymerase-iota (hPoliota), a member of the Y family of DNA polymerases, differs strikingly from other polymerases in its much higher proficiency and fidelity for nucleotide incorporation opposite template purines than opposite template pyrimidines. We present here a crystallographic analysis of hPoliota binary complexes, which together with the ternary complexes show that, contrary to replicative DNA polymerases, the DNA, and not the polymerase, undergoes the primary substrate-induced conformational change. The incoming dNTP "pushes" templates A and G from the anti to the syn conformation dictated by a rigid hPoliota active site. Together, the structures posit a mechanism for template selection wherein dNTP binding induces a conformational switch in template purines for productive Hoogsteen base pairing.

---

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
DNA polymerase iota	A	420	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
DNA template strand	T	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
DNA primer strand	P	7	N/A

Small Molecules

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: 2.4 Å
• R-Value Free: 0.276 
• R-Value Work: 0.228 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 98.367	α = 90.00
b = 98.367	β = 90.00
c = 202.497	γ = 120.00

Software Package:

Software Name	Purpose
AMoRE	phasing
HKL-2000	data reduction
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-06 
• Released Date: 2006-12-05 
• Deposition Author(s): Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

Revision History 

• Version 1.0: 2006-12-05
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance