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PDBsum entry 3mgi

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protein dna_rna ligands metals links
Lyase,transferase/DNA PDB id
3mgi
Jmol
Contents
Protein chain
319 a.a. *
DNA/RNA
Ligands
D3T
Metals
_NA
_MG
Waters ×156
* Residue conservation analysis
PDB id:
3mgi
Name: Lyase,transferase/DNA
Title: Ternary complex of a DNA polymerase lambda loop mutant
Structure: DNA polymerase lambda. Chain: a. Fragment: loop mutant of DNA polymerase lambda. Synonym: pol lambda, DNA polymerase kappa, DNA polymerase b beta2. Engineered: yes. Mutation: yes. DNA. Chain: t.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: poll. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
Resolution:
2.60Å     R-factor:   0.203     R-free:   0.270
Authors: M.Garcia-Diaz,K.Bebenek,R.Z.Zhou,L.F.Povirk,T.Kunkel
Key ref: K.Bebenek et al. (2010). Loop 1 modulates the fidelity of DNA polymerase lambda. Nucleic Acids Res, 38, 5419-5431. PubMed id: 20435673
Date:
06-Apr-10     Release date:   19-May-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UGP5  (DPOLL_HUMAN) -  DNA polymerase lambda
Seq:
Struc:
 
Seq:
Struc:
575 a.a.
319 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
Bound ligand (Het Group name = D3T)
matches with 63.00% 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!
  Cellular component     nucleus   1 term 
  Biological process     DNA repair   1 term 
  Biochemical function     DNA binding     4 terms  

 

 
    reference    
 
 
Nucleic Acids Res 38:5419-5431 (2010)
PubMed id: 20435673  
 
 
Loop 1 modulates the fidelity of DNA polymerase lambda.
K.Bebenek, M.Garcia-Diaz, R.Z.Zhou, L.F.Povirk, T.A.Kunkel.
 
  ABSTRACT  
 
Differences in the substrate specificity of mammalian family X DNA polymerases are proposed to partly depend on a loop (loop 1) upstream of the polymerase active site. To examine if this is the case in DNA polymerase lambda (pol lambda), here we characterize a variant of the human polymerase in which nine residues of loop 1 are replaced with four residues from the equivalent position in pol beta. Crystal structures of the mutant enzyme bound to gapped DNA with and without a correct dNTP reveal that the change in loop 1 does not affect the overall structure of the protein. Consistent with these structural data, the mutant enzyme has relatively normal catalytic efficiency for correct incorporation, and it efficiently participates in non-homologous end joining of double-strand DNA breaks. However, DNA junctions recovered from end-joining reactions are more diverse than normal, and the mutant enzyme is substantially less accurate than wild-type pol lambda in three different biochemical assays. Comparisons of the binary and ternary complex crystal structures of mutant and wild-type pol lambda suggest that loop 1 modulates pol lambda's fidelity by controlling dNTP-induced movements of the template strand and the primer-terminal 3'-OH as the enzyme transitions from an inactive to an active conformation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
21258395 S.S.Lange, K.Takata, and R.D.Wood (2011).
DNA polymerases and cancer.
  Nat Rev Cancer, 11, 96.  
21081096 Y.Li, and T.Schlick (2010).
Modeling DNA polymerase μ motions: subtle transitions before chemistry.
  Biophys J, 99, 3463-3472.  
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.