› 3slp

X-ray diffraction
2.3Å resolution

Crystal Structure of Lambda Exonuclease in Complex with a 12 BP Symmetric DNA Duplex

Released:
DOI: 10.2210/pdb3slp/pdb
PDB entry 3slp coloured by chain, front view.
PDB entry 3slp coloured by chain, side view.
PDB entry 3slp coloured by chain, top view.
Source organism: Lambdavirus lambda
Primary publication:
Crystal structures of lambda exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity.
Zhang J, McCabe KA, Bell CE
Proc Natl Acad Sci U S A 108 11872-7 (2011)
PMID: 21730170

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116882 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Exonuclease Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 229 amino acids
Theoretical weight: 26.22 KDa
Source organism: Escherichia virus Lambda
Expression system: Escherichia coli
UniProt:
  • Canonical: P03697 (Residues: 1-226; Coverage: 100%)
Gene names: exo, red-alpha, redX
Sequence domains: YqaJ-like viral recombinase domain
Structure domains: Lambda Exonuclease; Chain A
5'-D(*GP*CP*GP*AP*CP*TP*AP*GP*TP*CP*GP*C)-3' Chains: D, E
Molecule details ›
Chains: D, E
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Lambdavirus lambda
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 3 x CA
Ligand PO4 3 x PO4
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P65
Unit cell:
a: 80.115Å b: 80.115Å c: 241.041Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.215 0.211 0.281
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Bacteriophage lambda: Early pioneer and still relevant.
Casjens et al. (2015)
3 more

3 mentions without citation

Crystal structures of lambda exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity.
Zhang et al. (2011)
2 more