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PDBsum entry 1zyq

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protein dna_rna ligands metals Protein-protein interface(s) links
Transferase/electron transport/DNA PDB id
1zyq
Jmol
Contents
Protein chains
680 a.a. *
105 a.a. *
DNA/RNA
Ligands
DAD
Metals
_MG ×3
Waters ×219
* Residue conservation analysis
PDB id:
1zyq
Name: Transferase/electron transport/DNA
Title: T7 DNA polymerase in complex with 8og and incoming ddatp
Structure: 5'- d( Cp Gp Ap Ap Ap Ap Cp Gp Ap Cp Gp Gp Cp Cp Ap Gp Tp Gp Cp Cp Ap (Ddg))-3'. Chain: p. Engineered: yes. Other_details: primer strand. 5'-d( Cp Cp Cp (8Og) p Cp Tp Gp Gp Cp Ap Cp Tp Gp Gp Cp Cp Gp Tp Cp Gp Tp Tp Tp Tp Cp G)-3'.
Source: Synthetic: yes. Enterobacteria phage t7. Organism_taxid: 10760. Gene: 5. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Escherichia coli. Organism_taxid: 562. Gene: trxa, fipa, tsnc.
Biol. unit: Tetramer (from PQS)
Resolution:
2.70Å     R-factor:   0.224     R-free:   0.272
Authors: L.G.Brieba,R.J.Kokoska,K.Bebenek,T.A.Kunkel,T.Ellenberger
Key ref:
L.G.Brieba et al. (2005). A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine. Structure (Camb), 13, 1653-1659. PubMed id: 16271888 DOI: 10.1016/j.str.2005.07.020
Date:
10-Jun-05     Release date:   22-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00581  (DPOL_BPT7) -  DNA-directed DNA polymerase
Seq:
Struc:
 
Seq:
Struc:
704 a.a.
680 a.a.*
Protein chain
Pfam   ArchSchema ?
P0AA25  (THIO_ECOLI) -  Thioredoxin-1
Seq:
Struc:
109 a.a.
105 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
Bound ligand (Het Group name = DAD)
matches with 61.00% similarity
+ DNA(n)
= diphosphate
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     viral reproduction   7 terms 
  Biochemical function     nucleic acid binding     10 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2005.07.020 Structure (Camb) 13:1653-1659 (2005)
PubMed id: 16271888  
 
 
A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine.
L.G.Brieba, R.J.Kokoska, K.Bebenek, T.A.Kunkel, T.Ellenberger.
 
  ABSTRACT  
 
8-oxo-7,8-dihydroguanosine (8oG) is a highly mutagenic DNA lesion that stably pairs with adenosine, forming 8oG(syn).dA(anti) Hoogsteen base pairs. DNA polymerases show different propensities to insert dCMP or dAMP opposite 8oG, but the molecular mechanisms that determine faithful or mutagenic bypass are poorly understood. Here, we report kinetic and structural data providing evidence that, in T7 DNA polymerase, residue Lys536 is responsible for attenuating the miscoding potential of 8oG. The Lys536Ala polymerase shows a significant increase in mutagenic 8oG bypass versus wild-type polymerase, and a crystal structure of the Lys536Ala mutant reveals a closed complex with an 8oG(syn).dATP mismatch in the polymerase active site, in contrast to the unproductive, open complex previously obtained by using wild-type polymerase. We propose that Lys536 acts as a steric and/or electrostatic filter that attenuates the miscoding potential of 8oG by normally interfering with the binding of 8oG in a syn conformation that pairs with dATP.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. A Structural Rationale for Mutagenic and Faithful Bypass of 8oG
(A) A surface representation of the 8oG(syn)·dATP mismatch in the active site of the Lys536A polymerase shows that the Lys536 side chain (gray) in the closed conformation of the fingers subdomain clashes with 8oG in the syn conformation. An alanine substitution at this position (blue) and the subtle repositioning of residue Ile540 (depicted in blue for the Lys536Ala mutant and in gray for the parental polymerase) accommodates the Hoogsteen pairing with dATP in the polymerase active site. The fingers subdomain is depicted as blue ribbons. The 8oG(syn) templating base (red) forms a Hoogsteen base pair with the incoming ddATP (gray). Two metal ions in the polymerase active site are depicted as yellow spheres.
(B) The crystal structure of the parental exo - T7 DNA polymerase mutant in complex with 8oG(anti)·dCTP shows a hydrogen bond donated by Lys536 to the O8 group of 8oG, stabilizing the anti conformation of 8oG for base pairing interactions with dCTP (Brieba et al., 2004). Substitution of Lys536 with alanine prevents this interaction and decreases the efficiency of dCMP insertion opposite 8oG (Table 1).
 
  The above figure is reprinted by permission from Cell Press: Structure (Camb) (2005, 13, 1653-1659) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20706627 G.Pastor-Palacios, E.Azuara-Liceaga, and L.G.Brieba (2010).
A nuclear family A DNA polymerase from Entamoeba histolytica bypasses thymine glycol.
  PLoS Negl Trop Dis, 4, e786.  
20411947 J.Beckman, M.Wang, G.Blaha, J.Wang, and W.H.Konigsberg (2010).
Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine .
  Biochemistry, 49, 4116-4125.
PDB codes: 3lzi 3lzj
20166748 M.Hogg, J.Rudnicki, J.Midkiff, L.Reha-Krantz, S.Doublié, and S.S.Wallace (2010).
Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69.
  Biochemistry, 49, 2317-2325.
PDB code: 3lds
21070945 T.D.Silverstein, R.Jain, R.E.Johnson, L.Prakash, S.Prakash, and A.K.Aggarwal (2010).
Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase η.
  Structure, 18, 1463-1470.
PDB codes: 3oha 3ohb
19492058 R.Vasquez-Del Carpio, T.D.Silverstein, S.Lone, M.K.Swan, J.R.Choudhury, R.E.Johnson, S.Prakash, L.Prakash, and A.K.Aggarwal (2009).
Structure of human DNA polymerase kappa inserting dATP opposite an 8-OxoG DNA lesion.
  PLoS One, 4, e5766.
PDB codes: 3hed 3in5
19200715 S.Schneider, S.Schorr, and T.Carell (2009).
Crystal structure analysis of DNA lesion repair and tolerance mechanisms.
  Curr Opin Struct Biol, 19, 87-95.  
17650502 H.R.Lee, S.A.Helquist, E.T.Kool, and K.A.Johnson (2008).
Importance of hydrogen bonding for efficiency and specificity of the human mitochondrial DNA polymerase.
  J Biol Chem, 283, 14402-14410.  
18072751 J.C.Delaney, and J.M.Essigmann (2008).
Biological properties of single chemical-DNA adducts: a twenty year perspective.
  Chem Res Toxicol, 21, 232-252.  
18276636 Z.F.Pursell, J.T.McDonald, C.K.Mathews, and T.A.Kunkel (2008).
Trace amounts of 8-oxo-dGTP in mitochondrial dNTP pools reduce DNA polymerase gamma replication fidelity.
  Nucleic Acids Res, 36, 2174-2181.  
17725985 M.A.Graziewicz, R.J.Bienstock, and W.C.Copeland (2007).
The DNA polymerase gamma Y955C disease variant associated with PEO and parkinsonism mediates the incorporation and translesion synthesis opposite 7,8-dihydro-8-oxo-2'-deoxyguanosine.
  Hum Mol Genet, 16, 2729-2739.  
17652324 M.de Vega, and M.Salas (2007).
A highly conserved Tyrosine residue of family B DNA polymerases contributes to dictate translesion synthesis past 8-oxo-7,8-dihydro-2'-deoxyguanosine.
  Nucleic Acids Res, 35, 5096-5107.  
17293403 Y.Wang, S.Reddy, W.A.Beard, S.H.Wilson, and T.Schlick (2007).
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta.
  Biophys J, 92, 3063-3070.  
17313689 Y.Wang, and T.Schlick (2007).
Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides.
  BMC Struct Biol, 7, 7.  
16271879 W.A.Beard, and S.H.Wilson (2005).
Syn-full behavior by T7 DNA polymerase.
  Structure, 13, 1580-1582.  
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.