5FFJ

Structure of a nuclease-deletion mutant of the Type ISP restriction-modification enzyme LlaGI in complex with a DNA substrate mimic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes

Kulkarni, M.Nirwan, N.van Aelst, K.Szczelkun, M.D.Saikrishnan, K.

(2016) Nucleic Acids Res. 44: 4396-4408

  • DOI: 10.1093/nar/gkw154

  • PubMed Abstract: 
  • Engineering restriction enzymes with new sequence specificity has been an unaccomplished challenge, presumably because of the complexity of target recognition. Here we report detailed analyses of target recognition by Type ISP restriction-modificatio ...

    Engineering restriction enzymes with new sequence specificity has been an unaccomplished challenge, presumably because of the complexity of target recognition. Here we report detailed analyses of target recognition by Type ISP restriction-modification enzymes. We determined the structure of the Type ISP enzyme LlaGI bound to its target and compared it with the previously reported structure of a close homologue that binds to a distinct target, LlaBIII. The comparison revealed that, although the two enzymes use almost a similar set of structural elements for target recognition, the residues that read the bases vary. Change in specificity resulted not only from appropriate substitution of amino acids that contacted the bases but also from new contacts made by positionally distinct residues directly or through a water bridge. Sequence analyses of 552 Type ISP enzymes showed that the structural elements involved in target recognition of LlaGI and LlaBIII were structurally well-conserved but sequentially less-conserved. In addition, the residue positions within these structural elements were under strong evolutionary constraint, highlighting the functional importance of these regions. The comparative study helped decipher a partial consensus code for target recognition by Type ISP enzymes.


    Organizational Affiliation

    Division of Biology, Indian Institute of Science Education and Research, Pune 411008, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endonuclease and methylase LlaGI
A, B
1406Lactococcus lactisMutation(s): 0 
Find proteins for Q93R01 (Lactococcus lactis)
Go to UniProtKB:  Q93R01
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T)-3')D,E23unidentified
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*AP*GP*CP*TP*AP*AP*TP*AP*GP*AP*CP*TP*GP*GP*AP*TP*GP*GP*AP*GP*G)-3')C,F23unidentified
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 87.400α = 90.00
b = 222.290β = 105.14
c = 117.410γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
Aimlessdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome DBT India AllianceIndia500048-Z-09-Z

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Data collection, Database references, Derived calculations