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PDBsum entry 2pfq

Go to PDB code: 
protein dna_rna ligands metals links
Transferase, lyase/DNA PDB id
2pfq
Jmol
Contents
Protein chain
324 a.a. *
DNA/RNA
Ligands
DCP
PPV
Metals
_MG
_NA ×2
_MN ×2
Waters ×230
* Residue conservation analysis
PDB id:
2pfq
Name: Transferase, lyase/DNA
Title: Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal
Structure: Template. Chain: t. Engineered: yes. Primer. Chain: p. Engineered: yes. Downstream primer. Chain: d. Engineered: yes.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: poll. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.256     R-free:   0.287
Authors: M.Garcia-Diaz,K.Bebenek,J.M.Krahn,L.C.Pedersen,T.A.Kunkel
Key ref: M.Garcia-Diaz et al. (2007). Role of the catalytic metal during polymerization by DNA polymerase lambda. DNA Repair (Amst), 6, 1333-1340. PubMed id: 17475573
Date:
05-Apr-07     Release date:   15-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UGP5  (DPOLL_HUMAN) -  DNA polymerase lambda
Seq:
Struc:
 
Seq:
Struc:
575 a.a.
324 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
Bound ligand (Het Group name = DCP)
matches with 68.00% similarity
+ DNA(n)
=
diphosphate
Bound ligand (Het Group name = PPV)
corresponds exactly
+ 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    
 
 
DNA Repair (Amst) 6:1333-1340 (2007)
PubMed id: 17475573  
 
 
Role of the catalytic metal during polymerization by DNA polymerase lambda.
M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel.
 
  ABSTRACT  
 
The incorporation of dNMPs into DNA by polymerases involves a phosphoryl transfer reaction hypothesized to require two divalent metal ions. Here we investigate this hypothesis using as a model human DNA polymerase lambda (Pol lambda), an enzyme suggested to be activated in vivo by manganese. We report the crystal structures of four complexes of human Pol lambda. In a 1.9 A structure of Pol lambda containing a 3'-OH and the non-hydrolyzable analog dUpnpp, a non-catalytic Na+ ion occupies the site for metal A and the ribose of the primer-terminal nucleotide is found in a conformation that positions the acceptor 3'-OH out of line with the alpha-phosphate and the bridging oxygen of the pyrophosphate leaving group. Soaking this crystal in MnCl2 yielded a 2.0 A structure with Mn2+ occupying the site for metal A. In the presence of Mn2+, the conformation of the ribose is C3'-endo and the 3'-oxygen is in line with the leaving oxygen, at a distance from the phosphorus atom of the alpha-phosphate (3.69 A) consistent with and supporting a catalytic mechanism involving two divalent metal ions. Finally, soaking with MnCl2 converted a pre-catalytic Pol lambda/Na+ complex with unreacted dCTP in the active site into a product complex via catalysis in the crystal. These data provide pre- and post-transition state information and outline in a single crystal the pathway for the phosphoryl transfer reaction carried out by DNA polymerases.
 

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
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
21321236 M.L.Gleghorn, E.K.Davydova, R.Basu, L.B.Rothman-Denes, and K.S.Murakami (2011).
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
  Proc Natl Acad Sci U S A, 108, 3566-3571.
PDB codes: 3q0a 3q22 3q23 3q24
19631767 J.Yamtich, and J.B.Sweasy (2010).
DNA polymerase family X: function, structure, and cellular roles.
  Biochim Biophys Acta, 1804, 1136-1150.  
19502493 F.Romain, I.Barbosa, J.Gouge, F.Rougeon, and M.Delarue (2009).
Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region.
  Nucleic Acids Res, 37, 4642-4656.  
18984581 M.G.Pence, P.Blans, C.N.Zink, T.Hollis, J.C.Fishbein, and F.W.Perrino (2009).
Lesion bypass of N2-ethylguanine by human DNA polymerase iota.
  J Biol Chem, 284, 1732-1740.
PDB codes: 3epg 3epi
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.