PDBsum entry 1d2g

Transferase

PDB id: 1d2g

Contents

Protein chains

292 a.a. *

Waters ×318

* Residue conservation analysis

PDB id:

1d2g

Name:

Transferase

Title:

Crystal structure of r175k mutant glycine n-methyltransferase from rat liver

Structure:

Glycine n-methyltransferase. Chain: a, b. Fragment: whole enzyme. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Tissue: liver. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.194 R-free: 0.266

Authors:

Y.Huang,J.Komoto,F.Takusagawa,K.Konishi,Y.Takata

Key ref:

Y.Huang et al. (2000). Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes. J Mol Biol, 298, 149-162. PubMed id: 10756111 DOI: 10.1006/jmbi.2000.3637

Date:

08-Oct-99 Release date: 25-Oct-99

Protein chains

P13255  (GNMT_RAT) -  Glycine N-methyltransferase from Rattus norvegicus

Seq: 293 a.a.

Struc: 292 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.1.1.20 - glycine N-methyltransferase.
• Reaction: glycine + S-adenosyl-L-methionine = sarcosine + S-adenosyl-L-homocysteine + H⁺

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

reference

DOI no: 10.1006/jmbi.2000.3637

J Mol Biol 298:149-162 (2000)

PubMed id: 10756111

Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes.

Y.Huang, J.Komoto, K.Konishi, Y.Takata, H.Ogawa, T.Gomi, M.Fujioka, F.Takusagawa.

ABSTRACT

Glycine N-methyltransferase (S-adenosyl-l-methionine: glycine methyltransferase, EC 2.1.1.20; GNMT) catalyzes the AdoMet-dependent methylation of glycine to form sarcosine (N-methylglycine). Unlike most methyltransferases, GNMT is a tetrameric protein showing a positive cooperativity in AdoMet binding and weak inhibition by S-adenosylhomocysteine (AdoHcy). The first crystal structure of GNMT complexed with AdoMet showed a unique "closed" molecular basket structure, in which the N-terminal section penetrates and corks the entrance of the adjacent subunit. Thus, the apparent entrance or exit of the active site is not recognizable in the subunit structure, suggesting that the enzyme must possess a second, enzymatically active, "open" structural conformation. A new crystalline form of the R175K enzyme has been grown in the presence of an excess of AdoHcy, and its crystal structure has been determined at 3.0 A resolution. In this structure, the N-terminal domain (40 amino acid residues) of each subunit has moved out of the active site of the adjacent subunit, and the entrances of the active sites are now opened widely. An AdoHcy molecule has entered the site occupied in the "closed" structure by Glu15 and Gly16 of the N-terminal domain of the adjacent subunit. An AdoHcy binds to the consensus AdoMet binding site observed in the other methyltransferase. This AdoHcy binding site supports the glycine binding site (Arg175) deduced from a chemical modification study and site-directed mutagenesis (R175K). The crystal structures of WT and R175K enzymes were also determined at 2.5 A resolution. These enzyme structures have a closed molecular basket structure and are isomorphous to the previously determined AdoMet-GNMT structure. By comparing the open structure to the closed structure, mechanisms for auto-inhibition and for the forced release of the product AdoHcy have been revealed in the GNMT structure. The N-terminal section of the adjacent subunit occupies the AdoMet binding site and thus inhibits the methyltransfer reaction, whereas the same N-terminal section forces the departure of the potentially potent inhibitor AdoHcy from the active site and thus facilitates the methyltransfer reaction. Consequently GNMT is less active at a low level of AdoMet concentration, and is only weakly inhibited by AdoHcy. These properties of GNMT are particularly suited for regulation of the cellular AdoMet/AdoHcy ratio.

Selected figure(s)

Figure 2.
Figure 2. Subunit structures in (a) R175K closed structure and (b) AdoHcy-R175K open structure. The N-terminal domain, C-terminal domain and S-domain are illustrated by red, cyan and green, respectively. The U-loop of the adjacent subunit is shown by thick magenta coil. In the open structure, the N-terminal domain is invisible and an AdoHcy molecule (red) binds to the consensus AdoMet-binding site.

Figure 7.
Figure 7. Schematic diagrams of interaction of AdoHcy in the active site. It is noted that Trp117 stacks with the adenine ring.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 298, 149-162) copyright 2000.

Figures were selected by an automated process.