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PDBsum entry 1zet
Go to PDB code: 
protein dna_rna ligands metals links
Replication/DNA PDB id
1zet

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
388 a.a. *
DNA/RNA
Ligands
TTP
Metals
_MG
Waters ×168
* Residue conservation analysis
PDB id:
1zet
Name: Replication/DNA
Title: X-ray data do not support hoogsteen base-pairing during replication by human polymerase iota
Structure: 5'-d(p Ap Gp Gp Gp (Bru)p Cp Cp (Bru)p (Bru) p Cp Cp Cp Cp C)-3'. Chain: t. Engineered: yes. 5'-d( Gp Gp Gp Gp Gp Ap Ap Gp Gp Ap Cp Cp (Doc))-3'. Chain: p. Engineered: yes. Polymerase (DNA directed) iota. Chain: a.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: poli. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932
Biol. unit: Hexamer (from PQS)
Resolution:
2.30Å     R-factor:   0.261     R-free:   0.288
Authors: J.Wang
Key ref: J.Wang (2005). DNA polymerases: Hoogsteen base-pairing in DNA replication? Nature, 437, E6-7; discussion E7. PubMed id: 16163299
Date:
19-Apr-05     Release date:   19-Jul-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Q9UNA4  (POLI_HUMAN) -  DNA polymerase iota from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		740 a.a.
388 a.a.
Key:    Secondary structure  CATH domain

DNA/RNA chains
  A-G-G-G-BRU-C-C-BRU-BRU-C-C-C-C-C 14 bases
  G-G-G-G-G-A-A-G-G-A-C-C-DOC 13 bases

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
DNA(n)
 + 2'-deoxyribonucleoside 5'-triphosphate
 = DNA(n+1)
 + diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
Nature 437:E6-7; discussion E7 (2005)
PubMed id: 16163299  
 
 
DNA polymerases: Hoogsteen base-pairing in DNA replication?
J.Wang.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20936171 L.J.Stallons, and W.G.McGregor (2010).
Translesion synthesis polymerases in the prevention and promotion of carcinogenesis.
  J Nucleic Acids, 2010, 0.  
17898175 W.Yang, and R.Woodgate (2007).
What a difference a decade makes: insights into translesion DNA synthesis.
  Proc Natl Acad Sci U S A, 104, 15591-15598.  
17067213 J.B.Sweasy, J.M.Lauper, and K.A.Eckert (2006).
DNA polymerases and human diseases.
  Radiat Res, 166, 693-714.  
16615916 V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, and S.H.Wilson (2006).
Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
  Structure, 14, 757-766.
PDB codes: 2fmp 2fmq 2fms
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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