Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.77 kDa 
• Atom Count: 6,607 
• Modelled Residue Count: 708 
• Deposited Residue Count: 713 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 3SM4

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

• PDB DOI: 10.2210/pdb3SM4/pdb
• NDB: NA1195

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia virus Lambda
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-06-27 Released: 2011-07-20 
• Deposition Author(s): Bell, C.E., Zhang, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.186 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Literature

Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity.

Zhang, J., McCabe, K.A., Bell, C.E.

(2011) Proc Natl Acad Sci U S A 108: 11872-11877

• PubMed: 21730170 
• DOI: 10.1073/pnas.1103467108
• Primary Citation of Related Structures:  
  3SLP, 3SM4


• PubMed Abstract: 
  

The λ exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3' overhang. The crystal structure of λ exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of λ exonuclease in complex with DNA at 1.88-Å resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg(2+) ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5' phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of λ exonuclease operates not only at the level of the trimer, but also at the level of the monomer.

---

Organizational Affiliation: 

Ohio State Biochemistry Program and Department of Molecular and Cellular Biochemistry, The Ohio State University, 1645 Neil Avenue, Columbus, OH 43210, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exonuclease	A, B, C	229	Escherichia virus Lambda	Mutation(s): 1  Gene Names: exo, Lambda Exonuclease, red-alpha, redX EC: 3.1.11.3
UniProt
Find proteins for P03697 (Escherichia phage lambda) Explore P03697  Go to UniProtKB:  P03697

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3'	D	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3'	E	14	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A], J [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	I [auth B], K [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.186 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.391	α = 90
b = 78.391	β = 90
c = 247.534	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Bell, C.E., Zhang, J.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2011-08-03
  Changes: Database references, Experimental preparation, Structure summary
• Version 1.2: 2017-11-08
  Changes: Refinement description