1ZET

X-ray data do not support hoogsteen base-pairing during replication by human polymerase iota

• PDB DOI: https://doi.org/10.2210/pdb1ZET/pdb
• NAKB: 1ZET

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


• Deposited: 2005-04-19 Released: 2005-07-19 
• Deposition Author(s): Wang, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.261 
• R-Value Observed: 0.261 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1T3N

Literature

DNA polymerases: Hoogsteen base-pairing in DNA replication?

Wang, J.

(2005) Nature 437: E6-7; discussion E7

• PubMed: 16163299 
• DOI: https://doi.org/10.1038/nature04199
• Primary Citation of Related Structures:  
  1ZET


• PubMed Abstract: 
  

  Human polymerase-iota belongs to the error-prone Y family of polymerases, which frequently incorporate incorrect nucleotides during DNA replication but can efficiently bypass DNA lesions. On the basis of X-ray diffraction data, Nair et al. propose that Hoogsteen base-pairing is adopted by DNA during its replication by this enzyme. Here I re-examine their X-ray data and find that the electron density is very weak for a Hoogsteen base pair formed between a template adenine deoxyribonucleotide in the syn conformation and a deoxythymidine 5'-triphosphate (dTTP), and that the fit is better for a normal Watson-Crick base pair. As a guanine-cytosine (G-C) base pair has no potential to form a Hoogsteen base pair at physiological pH, Hoogsteen base-pairing is unlikely to be used in replication by this polymerase.

---

Organizational Affiliation: 

Center for Structural Biology, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.82 kDa 
• Atom Count: 3,816 
• Modelled Residue Count: 415 
• Deposited Residue Count: 415 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase (DNA directed) iota	C [auth A]	388	Homo sapiens	Mutation(s): 0  Gene Names: POLI
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNA4 (Homo sapiens) Explore Q9UNA4  Go to UniProtKB:  Q9UNA4
PHAROS:  Q9UNA4 GTEx:  ENSG00000101751

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(P*AP*GP*GP*GP*(BRU)P*CP*CP*(BRU)P*(BRU)P*CP*CP*CP*CP*C)-3'	A [auth T]	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*(DOC))-3'	B [auth P]	13	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.261 
• R-Value Observed: 0.261 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.831	α = 90
b = 98.831	β = 90
c = 202.755	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-19 
Deposition Author(s): Wang, J.

Revision History  

• Version 1.0: 2005-07-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-09-28
  Changes: Other
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations