1FJX

STRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASE MUTANT (T250G) IN COMPLEX WITH DNA AND ADOHCY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase.

Vilkaitis, G.Dong, A.Weinhold, E.Cheng, X.Klimasauskas, S.

(2000) J Biol Chem 275: 38722-38730

  • DOI: 10.1074/jbc.m005278200
  • Primary Citation of Related Structures:  
    1FJX

  • PubMed Abstract: 
  • DNA cytosine-5-methyltransferase HhaI recognizes the GCGC sequence and flips the inner cytosine out of DNA helix and into the catalytic site for methylation. The 5'-phosphate of the flipped out cytosine is in contact with the conserved Thr-250 from the target recognition domain ...

    DNA cytosine-5-methyltransferase HhaI recognizes the GCGC sequence and flips the inner cytosine out of DNA helix and into the catalytic site for methylation. The 5'-phosphate of the flipped out cytosine is in contact with the conserved Thr-250 from the target recognition domain. We have produced 12 mutants of Thr-250 and examined their methylation potential in vivo. Six active mutants were subjected to detailed biochemical and structural studies. Mutants with similar or smaller side chains (Ser, Cys, and Gly) are very similar to wild-type enzyme in terms of steady-state kinetic parameters k(cat), K(m)(DNA), K(m)(AdoMet). In contrast, the mutants with bulkier side chains (Asn, Asp, and His) show increased K(m) values for both substrates. Fluorescence titrations and stopped-flow kinetic analysis of interactions with duplex oligonucleotides containing 2-aminopurine at the target base position indicate that the T250G mutation leads to a more polar but less solvent-accessible position of the flipped out target base. The x-ray structure of the ternary M. HhaI(T250G).DNA.AdoHcy complex shows that the target cytosine is locked in the catalytic center of enzyme. The space created by the mutation is filled by water molecules and the adjacent DNA backbone atoms dislocate slightly toward the missing side chain. In aggregate, our results suggest that the side chain of Thr-250 is involved in constraining the conformation the DNA backbone and the target base during its rotation into the catalytic site of enzyme.


    Organizational Affiliation

    Institute of Biotechnology, Laboratory of Biological DNA Modification, LT-2028 Vilnius, Lithuania.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HHAI DNA METHYLTRANSFERASEC [auth A]327Haemophilus haemolyticusMutation(s): 1 
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
    DNA (5'-D(*TP*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 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SAH (Subject of Investigation/LOI)
    Query on SAH

    Download Ideal Coordinates CCD File 
    F [auth A]S-ADENOSYL-L-HOMOCYSTEINE
    C14 H20 N6 O5 S
    ZJUKTBDSGOFHSH-WFMPWKQPSA-N
     Ligand Interaction
    SO4
    Query on SO4

    Download Ideal Coordinates CCD File 
    D [auth A], E [auth A]SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    Binding Affinity Annotations 
    IDSourceBinding Affinity
    DNA PDBBind:  1FJX Kd: 1.4 (nM) from 1 assay(s)
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.26 Å
    • R-Value Free: 0.283 
    • R-Value Work: 0.207 
    • Space Group: H 3 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 98.46α = 90
    b = 98.46β = 90
    c = 323.22γ = 120
    Software Package:
    Software NamePurpose
    X-PLORrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2000-12-15
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2018-01-31
      Changes: Experimental preparation
    • Version 1.4: 2018-03-14
      Changes: Database references