3SM4

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


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 

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This is version 1.2 of the entry. See complete history


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

  • 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 ...

    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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ExonucleaseA, B, C229Escherichia virus LambdaMutation(s): 1 
Gene Names: exoLambda Exonucleasered-alpharedX
EC: 3.1.11.3
UniProt
Find proteins for P03697 (Escherichia phage lambda)
Explore P03697 
Go to UniProtKB:  P03697
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03697
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3'D12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3'E14N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
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 = 78.391α = 90
b = 78.391β = 90
c = 247.534γ = 120
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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