MGMT

Author: Christophe L.M.J. Verlinde
Revision date: 1/2/02

Name(s)

• Methylguanine-DNA Methyltransferase (MGMT)
• O6-Alkylguanine-DNA Alkyltransferase (AGT)

Function

Reverses endogenous alkylation at the O6-position of guanine.

Database entries

• ENZYME: 2.1.1.63
• BRENDA: 2.1.1.63
• OMIM: 156569
• BLINK: 34559
• PDB: 1EH6 - 1EH7 - 1EH8 - 1QNT
• Structural papers: PMID 10747039 - PMID 10606635
•  Mutation papers:  PMID 10487529

Structure analysis

Note: (*) The Zn(2+) was probably stripped during metal affinity purification procedures.

MGMT is a monomeric enzyme that possesses 2 domains. The N-terminal domain (residues 1-86) exhibits a Zn(2+) binding site, while the active site Cys 145 resides in the C-terminal domain. The zinc is located 20 Å away from the Cys, and has been shown to have little effect on the enzymatic activity. Its role is probably to provide extra stability to the protein (the zinc ligating residues are conserved). The C-terminal domain (86-207) harbors the catalytic site and provides a helix-turn-helix motif which probably inserts into the major groove of the substrate DNA; the recognition helix comprises residues 126-136.  (See image)

SNPs

The SNP associated residues as well as the active site Cys are indicated in Fig. 1.

  Figure 1: Location of SNP positions in the 3D-structure of MGMT. Also,
the N- and C-termini as well as the active site Cys 145 are indicated.
 

• L84F:

Structure: The wt residue is part of a loop and is embedded in a completely hydrophobic part of the protein (one of its neighbors is I143, another SNP list residue). The Leu to Phe mutation conserves the hydrophobicity. The larger volume of the Phe, about 28 A**3, can probably easily be accommodated by small atom shifts in the environment. Therefore, the L84F protein is expected to have the same structure as the wt.

Catalysis: Residue 84 is at a distance of 16 A from the active site Cys (CA-CA distance), and is not expected to affect the catalytic activity of MGMT significantly.  Because residue 84 is shielded from the protein surface, no effect on substrate binding is to be expected.

Interactions with protein partners: Because residue 84 is shielded from the protein surface, no effect on interactions with protein partners is to be expected.
 

• I143V

Structure: The wt residue is at the end of a type IV beta-turn and points in the same hydrophobic environment as L84. The Ile to Val mutation conserves the hydrophobicity. Small atom shifts probably adjust the local packing to accommodate the 25 A**3 smaller volume of Val. Therefore, the I143V protein is expected to have the same structure as the wt.

Catalysis: Residue 143 is at 6 A from the active site Cys (CA-CA distance), but the side chains of two residues are pointing into separate protein environments. Therefore, little effect on catalysis is expected. Because residue 143 is shielded from the protein surface, no effect on substrate binding is to be expected.

Interactions with protein partners: Because residue 143 is shielded from the protein surface, no effect on interactions with protein partners is to be expected.
 

• G160R

Structure: The wt residue, Gly,  is the 3rd residue of a type I beta-turn. Its phi/psi dihedral angles in the Ramachandran map, -95 and 13 degrees respectively, allow for substitution to non-Gly residues without changing these values. The G160R protein is expected to adopt the same structure as the wt.

Catalysis: Residue 160 is close to the active site of the enzyme. It lines the pocket that leads to the active site Cys 145 (Fig. 2a). A model of the G160R mutant (Fig. 2b) shows that the pocket becomes only somewhat smaller. Therefore, O6-alkylguanine should still be able to bind.  However, binding of positively charged ligands should become less favorable due to charge repulsion.

Fig. 2: (a) Substrate binding site of wt MGMT (left); (b) model of binding site in G160R mutant (right).
 

Interactions with DNA: Because of the positive charge of R160 the binding of DNA may be influenced.
 

• E166D

Structure: The wt residue is an exposed residue of an alpha helix. The conservative mutation to Asp is not expected to affect the protein structure.

Catalysis: Residue 166  is at 12 A from the active site Cys (CA-CA distance). Little effect on catalysis is expected.

Interactions with protein partners: ?
 

• K178R

Structure: Residue 178 occurs near the pseudo C-terminus of the protein. There the electron density ends in the crystal structures of 1EH6, 1EH7 and 1EH8, likely because of flexibiltiy of the C-terminus or proteolysis during crystallization. The 1QNT construct was created without C-terminus as it had been shown that its absence did not affect catalysis.

Catalysis: Residue 178  is at 12 A from the active site Cys (CA-CA distance). Little effect on catalysis is expected.

Interactions with protein partners: ?