› 3sm4

X-ray diffraction
1.88Å resolution

Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium

Released:
DOI: 10.2210/pdb3sm4/pdb
PDB entry 3sm4 coloured by chain, front view.
PDB entry 3sm4 coloured by chain, side view.
PDB entry 3sm4 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-116883 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Exonuclease Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 229 amino acids
Theoretical weight: 26.16 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(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Lambdavirus lambda
Expression system: Not provided
5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3' Chain: E
Molecule details ›
Chain: E
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: Lambdavirus lambda
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P65
Unit cell:
a: 78.391Å b: 78.391Å c: 247.534Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.161 0.16 0.186
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

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

11 mentions without citation

Structure and mechanism of the Red recombination system of bacteriophage λ.
Caldwell et al. (2019)
10 more