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PDBsum entry 3pml

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protein dna_rna ligands metals Protein-protein interface(s) links
Lyase,transferase/DNA PDB id
3pml
Jmol
Contents
Protein chains
322 a.a. *
DNA/RNA
Ligands
1GC ×2
Metals
_NA ×3
_MG ×4
Waters ×168
* Residue conservation analysis
PDB id:
3pml
Name: Lyase,transferase/DNA
Title: Crystal structure of a polymerase lambda variant with a dgtp opposite a templating t
Structure: DNA polymerase lambda. Chain: a, b. Fragment: unp residues 242-575. Synonym: pol lambda, DNA polymerase beta-2, pol beta2, DNA kappa. Engineered: yes. 5'-d( Cp Gp Gp Cp Tp Gp Tp Ap Cp Tp G)-3'. Chain: c, e. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Strain: 562. Gene: poll. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes
Resolution:
2.60Å     R-factor:   0.233     R-free:   0.271
Authors: K.Bebenek,L.C.Pedersen,T.A.Kunkel
Key ref: K.Bebenek et al. (2011). Replication infidelity via a mismatch with Watson-Crick geometry. Proc Natl Acad Sci U S A, 108, 1862-1867. PubMed id: 21233421
Date:
17-Nov-10     Release date:   26-Jan-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9UGP5  (DPOLL_HUMAN) -  DNA polymerase lambda
Seq:
Struc:
 
Seq:
Struc:
575 a.a.
322 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 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
+ 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    
 
 
Proc Natl Acad Sci U S A 108:1862-1867 (2011)
PubMed id: 21233421  
 
 
Replication infidelity via a mismatch with Watson-Crick geometry.
K.Bebenek, L.C.Pedersen, T.A.Kunkel.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22437501 N.Demeshkina, L.Jenner, E.Westhof, M.Yusupov, and G.Yusupova (2012).
A new understanding of the decoding principle on the ribosome.
  Nature, 484, 256-259.
PDB codes: 3tve 3tvf 3tvg 3tvh 3uyd 3uye 3uyf 3uyg 3uz1 3uz2 3uz3 3uz4 3uz6 3uz7 3uz8 3uz9 3uzf 3uzg 3uzh 3uzi 3uzk 3uzl 3uzm 3uzn
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.