PDBsum entry 1wsv

Transferase

PDB id: 1wsv

Contents

Protein chain

371 a.a. *

Ligands

SO4 ×11

THH ×2

Waters ×698

* Residue conservation analysis

PDB id:

1wsv

Name:

Transferase

Title:

Crystal structure of human t-protein of glycine cleavage system

Structure:

Aminomethyltransferase. Chain: a, b. Synonym: glycine cleavage system t protein, gcvt. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: gcst. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.60Å R-factor: 0.171 R-free: 0.245

Authors:

K.Okamura-Ikeda,H.Hosaka,M.Yoshimura,E.Yamashita,S.Toma,A.Nakagawa, K.Fujiwara,Y.Motokawa,H.Taniguchi

Key ref:

K.Okamura-Ikeda et al. (2005). Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia. J Mol Biol, 351, 1146-1159. PubMed id: 16051266 DOI: 10.1016/j.jmb.2005.06.056

Date:

11-Nov-04 Release date: 16-Aug-05

Protein chains

P48728  (GCST_HUMAN) -  Aminomethyltransferase, mitochondrial from Homo sapiens

Seq: 403 a.a.

Struc: 371 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.2.10 - aminomethyltransferase.
• Pathway: Glycine Cleavage System
• Reaction: N₆-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)- 5,6,7,8-tetrahydrofolate = N₆-[(R)-dihydrolipoyl]-L-lysyl-[protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4⁺

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

Added reference

DOI no: 10.1016/j.jmb.2005.06.056

J Mol Biol 351:1146-1159 (2005)

PubMed id: 16051266

Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia.

K.Okamura-Ikeda, H.Hosaka, M.Yoshimura, E.Yamashita, S.Toma, A.Nakagawa, K.Fujiwara, Y.Motokawa, H.Taniguchi.

ABSTRACT

T-protein, a component of the glycine cleavage system, catalyzes the formation of ammonia and 5,10-methylenetetrahydrofolate from the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein. Several mutations in the human T-protein gene cause non-ketotic hyperglycinemia. To gain insights into the effect of disease-causing mutations and the catalytic mechanism at the molecular level, crystal structures of human T-protein in free form and that bound to 5-methyltetrahydrofolate (5-CH3-H4folate) have been determined at 2.0 A and 2.6 A resolution, respectively. The overall structure consists of three domains arranged in a cloverleaf-like structure with the central cavity, where 5-CH3-H4folate is bound in a kinked shape with the pteridine group deeply buried into the hydrophobic pocket and the glutamyl group pointed to the C-terminal side surface. Most of the disease-related residues cluster around the cavity, forming extensive hydrogen bonding networks. These hydrogen bonding networks are employed in holding not only the folate-binding space but also the positions and the orientations of alpha-helix G and the following loop in the middle region, which seems to play a pivotal role in the T-protein catalysis. Structural and mutational analyses demonstrated that Arg292 interacts through water molecules with the folate polyglutamate tail, and that the invariant Asp101, located close to the N10 group of 5-CH3-H4folate, might play a key role in the initiation of the catalysis by increasing the nucleophilic character of the N10 atom of the folate substrate for the nucleophilic attack on the aminomethyl lipoate intermediate. A clever mechanism of recruiting the aminomethyl lipoate arm to the reaction site seems to function as a way of avoiding the release of toxic formaldehyde.

Selected figure(s)

Figure 3.
Figure 3. Schematic representation of the proposed aminomethyltransfer reaction catalyzed by T-protein. The bound H[4]folate attacks the methylene carbon of the aminomethyl lipoate arm attached to H-protein via the nucleophilic N10 group putatively with concomitant proton abstraction by Asp101 and ammonia release. The resulting covalent intermediate is attacked by the N5 group with concomitant deprotonation of the N5 by the sulfur group of the nascent dihydrolipoate. An alternative possibility is that the N5 group attacks first, followed by the attack of the N10 group.

Figure 5.
Figure 5. (a) NKH-related mutation sites mapped on the overall topology of huT. The mutant residues are depicted in a ball-and-stick representation with atoms colored in red. Residue numbers are labeled. (b) Stereo view of the hydrogen bonding networks as well as the putative functional residues in the huT reaction site. The side-chains of the NKH-related residues and residues hydrogen bonded to these are colored in red and green, respectively. The side-chains of the putative functional residues are colored in blue. Atoms, ligand and hydrogen bonds are colored as in Figure 1(b).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 351, 1146-1159) copyright 2005.

Figures were selected by an automated process.