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PDBsum entry 3c5f

Go to PDB code: 
protein dna_rna metals Protein-protein interface(s) links
Transferase, lyase/DNA PDB id
3c5f
Jmol
Contents
Protein chains
326 a.a. *
DNA/RNA
Metals
_NA ×6
Waters ×639
* Residue conservation analysis
PDB id:
3c5f
Name: Transferase, lyase/DNA
Title: Structure of a binary complex of the r517a pol lambda mutant
Structure: DNA polymerase lambda. Chain: a, b. Fragment: DNA binding region. Synonym: pol lambda, DNA polymerase kappa, DNA polymerase beta-2, pol beta2. Engineered: yes. Mutation: yes. DNA (5'- d( Dcp Dgp Dgp Dcp Dcp Dgp Dtp Dap Dcp Dtp Dg)-3').
Source: Homo sapiens. Human. Gene: poll. Expressed in: escherichia coli. Synthetic: yes. Synthetic: yes
Resolution:
2.25Å     R-factor:   0.224     R-free:   0.263
Ensemble: 2 models
Authors: M.Garcia-Diaz,K.Bebenek,M.C.Foley,L.C.Pedersen,T.Schlick, T.A.Kunkel
Key ref: K.Bebenek et al. (2008). Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda. EMBO Rep, 9, 459-464. PubMed id: 18369368
Date:
31-Jan-08     Release date:   02-Sep-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9UGP5  (DPOLL_HUMAN) -  DNA polymerase lambda
Seq:
Struc:
 
Seq:
Struc:
575 a.a.
326 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
+ 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!
  Cellular component     nucleus   1 term 
  Biological process     DNA repair   1 term 
  Biochemical function     DNA binding     4 terms  

 

 
    reference    
 
 
EMBO Rep 9:459-464 (2008)
PubMed id: 18369368  
 
 
Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda.
K.Bebenek, M.Garcia-Diaz, M.C.Foley, L.C.Pedersen, T.Schlick, T.A.Kunkel.
 
  ABSTRACT  
 
The simple deletion of nucleotides is common in many organisms. It can be advantageous when it activates genes beneficial to microbial survival in adverse environments, and deleterious when it mutates genes relevant to survival, cancer or degenerative diseases. The classical idea is that simple deletions arise by strand slippage. A prime opportunity for slippage occurs during DNA synthesis, but it remains unclear how slippage is controlled during a polymerization cycle. Here, we report crystal structures and molecular dynamics simulations of mutant derivatives of DNA polymerase lambda bound to a primer-template during strand slippage. Relative to the primer strand, the template strand is in multiple conformations, indicating intermediates on the pathway to deletion mutagenesis. Consistent with these intermediates, the mutant polymerases generate single-base deletions at high rates. The results indicate that dNTP-induced template strand repositioning during conformational rearrangements in the catalytic cycle is crucial to controlling the rate of strand slippage.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21429821 A.L.Abdulovic, S.E.Hile, T.A.Kunkel, and K.A.Eckert (2011).
The in vitro fidelity of yeast DNA polymerase δ and polymerase ɛ holoenzymes during dinucleotide microsatellite DNA synthesis.
  DNA Repair (Amst), 10, 497-505.  
21233421 K.Bebenek, L.C.Pedersen, and T.A.Kunkel (2011).
Replication infidelity via a mismatch with Watson-Crick geometry.
  Proc Natl Acad Sci U S A, 108, 1862-1867.
PDB codes: 3pml 3pmn 3pnc
21226976 T.Schlick, R.Collepardo-Guevara, L.A.Halvorsen, S.Jung, and X.Xiao (2011).
Biomolecularmodeling and simulation: a field coming of age.
  Q Rev Biophys, 44, 191-228.  
19631767 J.Yamtich, and J.B.Sweasy (2010).
DNA polymerase family X: function, structure, and cellular roles.
  Biochim Biophys Acta, 1804, 1136-1150.  
19572669 M.C.Foley, and T.Schlick (2009).
Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates.
  J Phys Chem B, 113, 13035-13047.  
19701199 M.Garcia-Diaz, K.Bebenek, A.A.Larrea, J.M.Havener, L.Perera, J.M.Krahn, L.C.Pedersen, D.A.Ramsden, and T.A.Kunkel (2009).
Template strand scrunching during DNA gap repair synthesis by human polymerase lambda.
  Nat Struct Mol Biol, 16, 967-972.  
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.