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PDBsum entry 3k5a
Go to PDB code: 
protein dna_rna ligands metals links
Transferase/DNA PDB id
3k5a

 

 

 

 

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Contents
Protein chain
778 a.a. *
DNA/RNA
Ligands
DGT
Metals
_MG ×2
Waters ×434
* Residue conservation analysis
Obsolete entry
PDB id:
3k5a
Name: Transferase/DNA
Title: Crystal structure of e.Coli pol ii-normal DNA-dgtp ternary complex
Structure: DNA polymerase ii. Chain: a. Synonym: pol ii. Engineered: yes. Mutation: yes. DNA (5'- d( Tp Ap Cp Gp Tp Ap Cp Gp Cp Tp Ap Gp Gp Cp Ap Cp A)-3'). Chain: t. Engineered: yes.
Source: Escherichia coli k-12. Organism_taxid: 83333. Strain: k-12. Gene: b0060, dina, jw0059, polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Protease cleavage site. Synthetic: yes. Other_details: chemical synthesis.
Resolution:
2.40Å     R-factor:   0.224     R-free:   0.227
Authors: W.Yang,F.Wang
Key ref: F.Wang and W.Yang (2009). Structural insight into translesion synthesis by DNA Pol II. Cell, 139, 1279-1289. PubMed id: 20064374
Date:
06-Oct-09     Release date:   09-Feb-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21189  (DPO2_ECOLI) -  DNA polymerase II from Escherichia coli (strain K12)
Seq:
Struc: 		 
Seq:
Struc: 		783 a.a.
778 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains
  T-A-C-G-T-A-C-G-C-T-A-G-G-C-A-C-A 17 bases
  G-T-G-C-C-T-A-G-C-G-T-A-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)
Bound ligand (Het Group name = DGT)
matches with 62.50% similarity 		+ 2'-deoxyribonucleoside 5'-triphosphate
 = DNA(n+1)
 + diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
Cell 139:1279-1289 (2009)
PubMed id: 20064374  
 
 
Structural insight into translesion synthesis by DNA Pol II.
F.Wang, W.Yang.
 
  ABSTRACT  
 
E. coli DNA Pol II and eukaryotic Rev3 are B-family polymerases that can extend primers past a damaged or mismatched site when the high-fidelity replicative polymerases in the same family are ineffective. We report here the biochemical and structural properties of DNA Pol II that facilitate this translesion synthesis. DNA Pol II can extend primers past lesions either directly or by template skipping, in which small protein cavities outside of the active site accommodate looped-out template nucleotides 1 or 2 bp upstream. Because of multiple looping-out alternatives, mutation spectra of bypass synthesis are complicated. Moreover, translesion synthesis is enhanced by altered partitioning of DNA substrate between the polymerase active site and the proofreading exonuclease site. Compared to the replicative B family polymerases, DNA Pol II has subtle amino acid changes remote from the active site that allow it to replicate normal DNA with high efficiency yet conduct translesion synthesis when needed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22785315 T.Nakamura, Y.Zhao, Y.Yamagata, Y.J.Hua, and W.Yang (2012).
Watching DNA polymerase η make a phosphodiester bond.
  Nature, 487, 196-201.
PDB codes: 4ecq 4ecr 4ecs 4ect 4ecu 4ecv 4ecw 4ecx 4ecy 4ecz 4ed0 4ed1 4ed2 4ed3 4ed6 4ed7 4ed8
20577208 C.Biertümpfel, Y.Zhao, Y.Kondo, S.Ramón-Maiques, M.Gregory, J.Y.Lee, C.Masutani, A.R.Lehmann, F.Hanaoka, and W.Yang (2010).
Structure and mechanism of human DNA polymerase eta.
  Nature, 465, 1044-1048.
PDB codes: 3mr2 3mr3 3mr4 3mr5 3mr6 3si8
20921373 K.Datta, N.P.Johnson, and P.H.von Hippel (2010).
DNA conformational changes at the primer-template junction regulate the fidelity of replication by DNA polymerase.
  Proc Natl Acad Sci U S A, 107, 17980-17985.  
20154704 O.Rechkoblit, A.Kolbanovskiy, L.Malinina, N.E.Geacintov, S.Broyde, and D.J.Patel (2010).
Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4.
  Nat Struct Mol Biol, 17, 379-388.
PDB codes: 3khg 3khh 3khl 3khr
  20936174 S.Chandani, C.Jacobs, and E.L.Loechler (2010).
Architecture of y-family DNA polymerases relevant to translesion DNA synthesis as revealed in structural and molecular modeling studies.
  J Nucleic Acids, 2010, 0.  
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
21070511 T.Narita, T.Tsurimoto, J.Yamamoto, K.Nishihara, K.Ogawa, E.Ohashi, T.Evans, S.Iwai, S.Takeda, and K.Hirota (2010).
Human replicative DNA polymerase δ can bypass T-T (6-4) ultraviolet photoproducts on template strands.
  Genes Cells, 15, 1228-1239.  
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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