1SKM

HhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase

Horton, J.R.Ratner, G.Banavali, N.K.Huang, N.Choi, Y.Maier, M.A.Marquez, V.E.MacKerell, A.D.Cheng, X.

(2004) Nucleic Acids Res. 32: 3877-3886

  • DOI: 10.1093/nar/gkh701

  • PubMed Abstract: 
  • Rotation of a DNA or RNA nucleotide out of the double helix and into a protein pocket ('base flipping') is a mechanistic feature common to some DNA/RNA-binding proteins. Here, we report the structure of HhaI methyltransferase in complex with DNA cont ...

    Rotation of a DNA or RNA nucleotide out of the double helix and into a protein pocket ('base flipping') is a mechanistic feature common to some DNA/RNA-binding proteins. Here, we report the structure of HhaI methyltransferase in complex with DNA containing a south-constrained abasic carbocyclic sugar at the target site in the presence of the methyl donor byproduct AdoHcy. Unexpectedly, the locked south pseudosugar appears to be trapped in the middle of the flipping pathway via the DNA major groove, held in place primarily through Van der Waals contacts with a set of invariant amino acids. Molecular dynamics simulations indicate that the structural stabilization observed with the south-constrained pseudosugar will not occur with a north-constrained pseudosugar, which explains its lowered binding affinity. Moreover, comparison of structural transitions of the sugar and phosphodiester backbone observed during computational studies of base flipping in the M.HhaI-DNA-AdoHcy ternary complex indicate that the south-constrained pseudosugar induces a conformation on the phosphodiester backbone that corresponds to that of a discrete intermediate of the base-flipping pathway. As previous crystal structures of M.HhaI ternary complex with DNA displayed the flipped sugar moiety in the antipodal north conformation, we suggest that conversion of the sugar pucker from south to north beyond the middle of the pathway is an essential part of the mechanism through which flipping must proceed to reach its final destination. We also discuss the possibility of the south-constrained pseudosugar mimicking a transition state in the phosphodiester and sugar moieties that occurs during DNA base flipping in the presence of M.HhaI.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Modification methylase HhaI
A
327Haemophilus parahaemolyticusGene Names: hhaIM
EC: 2.1.1.37
Find proteins for P05102 (Haemophilus parahaemolyticus)
Go to UniProtKB:  P05102
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'C13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*T*GP*TP*CP*AP*GP*(HCX)P*GP*CP*AP*TP*GP*G)-3'D13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HCX
Query on HCX
D
NON-POLYMERC7 H13 O4 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 95.681α = 90.00
b = 95.681β = 90.00
c = 315.683γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CAD4data collection
SCALEPACKdata scaling
CAD4data reduction
GLRFphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance