PDBsum entry: 1skm

Transferase/DNA

PDB id: 1skm

Contents

Protein chain

327 a.a. *

DNA/RNA

Ligands

SAH

Waters ×257

* Residue conservation analysis

PDB id:

1skm

Name:

Transferase/DNA

Title:

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

Structure:

5'-d( Tp Cp Cp Ap Tp Gp Cp Gp Cp Tp Gp Ap C)-3'. Chain: c. Engineered: yes. 5'-d( T Gp Tp Cp Ap Gp (Hcx)p Gp Cp Ap Tp Gp G)- 3'. Chain: d. Engineered: yes. Modification methylase hhai. Chain: a.

Source:

Synthetic: yes. Haemophilus haemolyticus. Organism_taxid: 726. Gene: hhaim. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Trimer (from PQS)

Resolution:

2.20Å R-factor: 0.183 R-free: 0.221

Authors:

J.R.Horton,G.Ratner,N.Banavali,N.Huang,V.E.Marquez, A.D.Mackerell,X.Cheng

Key ref:

J.R.Horton et al. (2004). Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res, 32, 3877-3886. PubMed id: 15273274 DOI: 10.1093/nar/gkh701

Date:

05-Mar-04 Release date: 24-Aug-04

Protein chain

P05102  (MTH1_HAEPH) -  Modification methylase HhaI

Seq: 327 a.a.

Struc: 327 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.37 - Dna (cytosine-5-)-methyltransferase.
• Reaction: S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine

S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine (Bound ligand (Het Group name = SAH) corresponds exactly) + DNA containing 5-methylcytosine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: DNA restriction-modification system (2 terms)
• Biochemical function: transferase activity (4 terms)

reference

DOI no: 10.1093/nar/gkh701

Nucleic Acids Res 32:3877-3886 (2004)

PubMed id: 15273274

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

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

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 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.