PDBsum entry: 1o92

Transferase

PDB id: 1o92

Contents

Protein chains

368 a.a. *

Ligands

AMB

PO4 ×3

ADP

Metals

_MG ×3

__K ×2

Waters ×184

* Residue conservation analysis

PDB id:

1o92

Name:

Transferase

Title:

Methionine adenosyltransferase complexed with adp and a l-methionine analogous

Structure:

S-adenosylmethionine synthetase. Chain: a, b. Synonym: methionine adenosyltransferase, adomet synthetase, mat-i. Engineered: yes

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Organ: liver. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PDB file)

Resolution:

3.19Å R-factor: 0.246 R-free: 0.264

Authors:

B.Gonzalez,M.A.Pajares,J.A.Hermoso,J.Sanz-Aparicio

Key ref:

B.González et al. (2003). Crystal structures of methionine adenosyltransferase complexed with substrates and products reveal the methionine-ATP recognition and give insights into the catalytic mechanism. J Mol Biol, 331, 407-416. PubMed id: 12888348 DOI: 10.1016/S0022-2836(03)00728-9

Date:

10-Dec-02 Release date: 07-Aug-03

Protein chains

P13444  (METK1_RAT) -  S-adenosylmethionine synthase isoform type-1

Seq: 397 a.a.

Struc: 368 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.6 - Methionine adenosyltransferase.
• Pathway: Methionine Adenosyltransferase
• Reaction: ATP + L-methionine + H₂O = phosphate + diphosphate + S-adenosyl-L- methionine

ATP (Bound ligand (Het Group name = ADP) matches with 87.00% similarity) + L-methionine (Bound ligand (Het Group name = AMB) matches with 63.00% similarity) + H(2)O = phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) + diphosphate + S-adenosyl-L- methionine

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

 Gene Ontology (GO) functional annotation 

• Biological process: one-carbon metabolic process (4 terms)
• Biochemical function: nucleotide binding (9 terms)

reference

DOI no: 10.1016/S0022-2836(03)00728-9

J Mol Biol 331:407-416 (2003)

PubMed id: 12888348

Crystal structures of methionine adenosyltransferase complexed with substrates and products reveal the methionine-ATP recognition and give insights into the catalytic mechanism.

B.González, M.A.Pajares, J.A.Hermoso, D.Guillerm, G.Guillerm, J.Sanz-Aparicio.

ABSTRACT

Methionine adenosyltransferases (MATs) are a family of enzymes in charge of synthesising S-adenosylmethionine (SAM), the most important methyl donor present in living organisms. These enzymes use methionine and ATP as reaction substrates, which react in a S(N)2 fashion where the sulphur atom from methionine attacks C5' from ATP while triphosphate chain is cleaved. A MAT liver specific isoenzyme has been detected, which exists in two distinct oligomeric forms, a dimer (MAT III) and a tetramer (MAT I). Our previously reported crystal structure of MAT I complexed with an inhibitor led to the identification of the methionine-binding site. We present here the results obtained from the complex of MAT I with a competitive inhibitor of methionine, (2S,4S)-amino-4,5-epoxypentanoic acid (AEP), which presents the same features at the methionine binding site reported before. We have also analysed several complexes of this enzyme with methionine and ATP and analogues of them, in order to characterise the interaction that is produced between both substrates. The crystal structures of the complexes reveal how the substrates recognise each other at the active site of the enzyme, and suggest a putative binding site for the product SAM. The residues involved in the interactions of substrates and products with MAT have been identified, and the results agree with all the previous data concerning mutagenesis experiments and crystallographic work. Moreover, all the information provided from the analysis of the complexes has allowed us to postulate a catalytic mechanism for this family of enzymes. In particular, we propose a key role for Lys182 in the correct positioning of the substrates, and Asp135(*), in stabilising the sulphonium group formed in the product (SAM).

Selected figure(s)

Figure 2.
Figure 2. The MAT I-AEP complex: (a) MAT I tetramer with the ligands and metal ions represented in ball-and-stick. The subunit of each dimer is coloured in cyan and blue. (b) A detail of the active site showing the three phosphate positions, and the inhibitor AEP. The loop (251-260) involved in methionine binding is in yellow, and the putative metal are represented as spheres, Mg2+ in orange, and K+ in magenta. (c) Detail of the proposed atomic interactions: the methionine analogue stacks against Phe251 in a rather planar conformation. A carboxylate oxygen atom is co-ordinating a Mg2+ (Mgm), which in turn is linked to Asp180. A second Mg2+ cation (Mg3) is linked to Asp135^* of the other subunit and is further co-ordinated to a phosphate anion (Pi3). The final 2F[o] -F[c] electron density map at the AEP and the ions is contoured at 1s. Co-ordination of both Mg2+ ions must be completed with water molecules not visible in the electron density.

Figure 6.
Figure 6. Molecular surface at the active site of MAT I showing (a) the substrates ATP and methionine in grey and (b) the ADP molecule in cyan. The phosphate ions are shown in yellow and two Mg2+ are represented as magenta spheres. As it can be seen, the ADP is in a different orientation from that of ATP, suggesting that the product reorients in the active site after reaction is produced and before it is released. (c) Proposed enzymatic mechanism and superposition of the different states: the binding of ATP and Met, as observed in the crystal (a) is represented in dark grey and the putative SAM, superimposed to ADP found in the crystal (b), is represented in cyan. A model for the proposed "reactive" conformation of ATP is shown in white. In this model, ATP-Pg remains at the position coincident with Pi2, while ATP-Pa is situated at Pi3 (both P[i] sites are circled in yellow).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 407-416) copyright 2003.

Figures were selected by an automated process.