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


  • 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 t ...

    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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HHAI DNA METHYLTRANSFERASE
A
327Haemophilus parahaemolyticusMutation(s): 1 
Gene Names: hhaIM
EC: 2.1.1.37
Find proteins for P05102 (Haemophilus parahaemolyticus)
Go to UniProtKB:  P05102
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3')C,D13N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 1.4 nM PDBBIND
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 = 98.460α = 90.00
b = 98.460β = 90.00
c = 323.220γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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