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PDBsum entry 2ozm

Go to PDB code: 
protein dna_rna ligands metals links
Transferase/DNA PDB id
2ozm
Jmol
Contents
Protein chain
903 a.a. *
DNA/RNA
Ligands
N5P
Metals
_MG
Waters ×400
* Residue conservation analysis
PDB id:
2ozm
Name: Transferase/DNA
Title: Crystal structure of rb69 gp43 in complex with DNA with 5- nitp opposite an abasic site analog
Structure: DNA polymerase. Chain: a. Engineered: yes. Mutation: yes. Template DNA. Chain: t. Synonym: gp43. Engineered: yes. Primer DNA.
Source: Enterobacteria phage rb69. Organism_taxid: 12353. Gene: 43. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes
Resolution:
2.86Å     R-factor:   0.210     R-free:   0.268
Authors: K.E.Zahn,H.Belrhali,S.S.Wallace,S.Doublie
Key ref: K.E.Zahn et al. (2007). Caught bending the A-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide. Biochemistry, 46, 10551-10561. PubMed id: 17718515
Date:
26-Feb-07     Release date:   23-Oct-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q38087  (DPOL_BPR69) -  DNA polymerase
Seq:
Struc:
 
Seq:
Struc:
903 a.a.
903 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: 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 = N5P)
matches with 60.00% 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     DNA biosynthetic process   4 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
    reference    
 
 
Biochemistry 46:10551-10561 (2007)
PubMed id: 17718515  
 
 
Caught bending the A-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide.
K.E.Zahn, H.Belrhali, S.S.Wallace, S.Doublié.
 
  ABSTRACT  
 
Damage to DNA involving excision of the nucleobase at the N-glycosidic bond forms abasic sites. If a nucleotide becomes incorporated opposite an unrepaired abasic site during DNA synthesis, most B family polymerases obey the A-rule and preferentially incorporate dAMP without instruction from the template. In addition to being potentially mutagenic, abasic sites provide strong blocks to DNA synthesis. A previous crystal structure of an exonuclease deficient variant of the replicative B family DNA polymerase from bacteriophage RB69 (RB69 gp43 exo-) illustrated these properties, showing that the polymerase failed to translocate the DNA following insertion of dAMP opposite an abasic site. We examine four new structures depicting several steps of translesion DNA synthesis by RB69 gp43 exo-, employing a non-natural purine triphosphate analogue, 5-nitro-1-indolyl-2'-deoxyriboside-5'-triphosphate (5-NITP), that is incorporated more efficiently than dAMP opposite abasic sites. Our structures indicate that a dipole-induced dipole stacking interaction between the 5-nitro group and base 3' to the templating lesion explains the enhanced kinetics of 5-NITP. As with dAMP, the DNA fails to translocate following insertion of 5-NIMP, although distortions at the nascent primer terminus contribute less than previously thought in inducing the stall, given that 5-NIMP preserves relatively undistorted geometry at the insertion site following phosphoryl transfer. An open ternary configuration, novel in B family polymerases, reveals an initial template independent binding of 5-NITP adjacent to the active site of the open polymerase, suggesting that closure of the fingers domain shuttles the nucleotide to the active site while testing the substrate against the template.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22266819 K.Das, S.E.Martinez, J.D.Bauman, and E.Arnold (2012).
HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
  Nat Struct Mol Biol, 19, 253-259.
PDB codes: 3v4i 3v6d 3v81
20952399 E.A.Motea, I.Lee, and A.J.Berdis (2011).
Quantifying the energetic contributions of desolvation and {pi}-electron density during translesion DNA synthesis.
  Nucleic Acids Res, 39, 1623-1637.  
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
20166752 P.Aller, Y.Ye, S.S.Wallace, C.J.Burrows, and S.Doublié (2010).
Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin.
  Biochemistry, 49, 2502-2509.
PDB code: 3l8b
21059936 S.J.Hyde, B.E.Eckenroth, B.A.Smith, W.A.Eberley, N.H.Heintz, J.E.Jackman, and S.Doublié (2010).
tRNA(His) guanylyltransferase (THG1), a unique 3'-5' nucleotidyl transferase, shares unexpected structural homology with canonical 5'-3' DNA polymerases.
  Proc Natl Acad Sci U S A, 107, 20305-20310.
PDB codes: 3otb 3otc 3otd 3ote
20400942 S.Obeid, N.Blatter, R.Kranaster, A.Schnur, K.Diederichs, W.Welte, and A.Marx (2010).
Replication through an abasic DNA lesion: structural basis for adenine selectivity.
  EMBO J, 29, 1738-1747.
PDB codes: 3lwl 3lwm
19778048 D.Loakes, J.Gallego, V.B.Pinheiro, E.T.Kool, and P.Holliger (2009).
Evolving a polymerase for hydrophobic base analogues.
  J Am Chem Soc, 131, 14827-14837.  
19368886 D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, and A.K.Aggarwal (2009).
DNA synthesis across an abasic lesion by human DNA polymerase iota.
  Structure, 17, 530-537.
PDB codes: 3g6v 3g6x 3g6y
19759017 W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, and S.H.Wilson (2009).
DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".
  J Biol Chem, 284, 31680-31689.
PDB codes: 3isb 3isc 3isd
18652487 A.Sheriff, E.Motea, I.Lee, and A.J.Berdis (2008).
Mechanism and dynamics of translesion DNA synthesis catalyzed by the Escherichia coli Klenow fragment.
  Biochemistry, 47, 8527-8537.  
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.  
18503083 X.Zhong, L.C.Pedersen, and T.A.Kunkel (2008).
Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity.
  Nucleic Acids Res, 36, 3892-3904.
PDB code: 3cq8
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.