2I9K

Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.287 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI

Youngblood, B.Shieh, F.K.De Los Rios, S.Perona, J.J.Reich, N.O.

(2006) J Mol Biol 362: 334-346

  • DOI: 10.1016/j.jmb.2006.07.031
  • Primary Citation of Related Structures:  
    2I9K

  • PubMed Abstract: 
  • Improved sequence specificity of the DNA cytosine methyltransferase HhaI was achieved by disrupting interactions at a hydrophobic interface between the active site of the enzyme and a highly conserved flexible loop. Transient fluorescence experiments show that mutations disrupting this interface destabilize the positioning of the extrahelical, "flipped" cytosine base within the active site ...

    Improved sequence specificity of the DNA cytosine methyltransferase HhaI was achieved by disrupting interactions at a hydrophobic interface between the active site of the enzyme and a highly conserved flexible loop. Transient fluorescence experiments show that mutations disrupting this interface destabilize the positioning of the extrahelical, "flipped" cytosine base within the active site. The ternary crystal structure of the F124A M.HhaI bound to cognate DNA and the cofactor analogue S-adenosyl-l-homocysteine shows an increase in cavity volume between the flexible loop and the core of the enzyme. This cavity disrupts the interface between the loop and the active site, thereby destabilizing the extrahelical target base. The favored partitioning of the base-flipped enzyme-DNA complex back to the base-stacked intermediate results in the mutant enzyme discriminating better than the wild-type enzyme against non-cognate sites. Building upon the concepts of kinetic proofreading and our understanding of M.HhaI, we describe how a 16-fold specificity enhancement achieved with a double mutation at the loop/active site interface is acquired through destabilization of intermediates prior to methyltransfer rather than disruption of direct interactions between the enzyme and the substrate for M.HhaI.


    Organizational Affiliation

    Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106-9510, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Modification methylase HhaIC [auth A]327Haemophilus haemolyticusMutation(s): 1 
Gene Names: hhaIM
EC: 2.1.1.73 (PDB Primary Data), 2.1.1.37 (UniProt)
UniProt
Find proteins for P05102 (Haemophilus parahaemolyticus)
Explore P05102 
Go to UniProtKB:  P05102
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*T*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3'A [auth C], B [auth D]13N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SAH (Subject of Investigation/LOI)
    Query on SAH

    Download Ideal Coordinates CCD File 
    D [auth A]S-ADENOSYL-L-HOMOCYSTEINE
    C14 H20 N6 O5 S
    ZJUKTBDSGOFHSH-WFMPWKQPSA-N
     Ligand Interaction
    Binding Affinity Annotations 
    IDSourceBinding Affinity
    DNA PDBBind:  2I9K Kd: 0.3 (nM) from 1 assay(s)
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.65 Å
    • R-Value Free: 0.262 
    • R-Value Work: 0.238 
    • R-Value Observed: 0.287 
    • Space Group: H 3 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 97.51α = 90
    b = 97.51β = 90
    c = 319.7γ = 120
    Software Package:
    Software NamePurpose
    MOSFLMdata reduction
    CNSrefinement
    CCP4data scaling
    CNSphasing

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2006-10-10
      Type: Initial release
    • Version 1.1: 2008-05-01
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2021-10-20
      Changes: Database references, Derived calculations