PDBsum entry: 2h23

Transferase

PDB id: 2h23

Contents

Protein chains

424 a.a. *

Ligands

SAH ×3

M3L ×3

Waters ×390

* Residue conservation analysis

PDB id:

2h23

Name:

Transferase

Title:

Structure of rubisco lsmt bound to trimethyllysine and adohc

Structure:

Ribulose-1,5 bisphosphate carboxylase/oxygenase l subunit n-methyltransferase. Chain: a, b, c. Fragment: rubisco lsmt (residues 49-482). Synonym: [ribulose- bisphosphate carboxylase]-lysine n- methyltransferase, rubisco methyltransferase, rubisco lsmt, engineered: yes

Source:

Pisum sativum. Pea. Organism_taxid: 3888. Gene: rbcmt. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Trimer (from PQS)

Resolution:

2.45Å R-factor: 0.253 R-free: 0.288

Authors:

J.F.Couture,G.Hauk,R.C.Trievel

Key ref:

J.F.Couture et al. (2006). Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases. J Biol Chem, 281, 19280-19287. PubMed id: 16682405 DOI: 10.1074/jbc.M602257200

Date:

17-May-06 Release date: 30-May-06

Protein chains

Q43088  (RBCMT_PEA) -  Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic

Seq: 489 a.a.

Struc: 424 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.1.1.127 - [Ribulose-bisphosphate carboxylase]-lysine N-methyltransferase.
• Reaction: S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine = S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]- N₆-methyl-L-lysine

S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine = S-adenosyl-L-homocysteine (Bound ligand (Het Group name = SAH) corresponds exactly) + [ribulose-1,5-bisphosphate carboxylase]- N(6)-methyl-L-lysine (Bound ligand (Het Group name = M3L) matches with 55.56% similarity)

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: protein binding (1 term)

reference

DOI no: 10.1074/jbc.M602257200

J Biol Chem 281:19280-19287 (2006)

PubMed id: 16682405

Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases.

J.F.Couture, G.Hauk, M.J.Thompson, G.M.Blackburn, R.C.Trievel.

ABSTRACT

SET domain enzymes represent a distinct family of protein lysine methyltransferases in eukaryotes. Recent studies have yielded significant insights into the structural basis of substrate recognition and the product specificities of these enzymes. However, the mechanism by which SET domain methyltransferases catalyze the transfer of the methyl group from S-adenosyl-L-methionine to the lysine epsilon-amine has remained unresolved. To elucidate this mechanism, we have determined the structures of the plant SET domain enzyme, pea ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit methyltransferase, bound to S-adenosyl-L-methionine, and its non-reactive analogs Aza-adenosyl-L-methionine and Sinefungin, and characterized the binding of these ligands to a homolog of the enzyme. The structural and biochemical data collectively reveal that S-adenosyl-L-methionine is selectively recognized through carbon-oxygen hydrogen bonds between the cofactor's methyl group and an array of structurally conserved oxygens that comprise the methyl transfer pore in the active site. Furthermore, the structure of the enzyme co-crystallized with the product epsilon-N-trimethyllysine reveals a trigonal array of carbon-oxygen interactions between the epsilon-ammonium methyl groups and the oxygens in the pore. Taken together, these results establish a central role for carbon-oxygen hydrogen bonding in aligning the cofactor's methyl group for transfer to the lysine epsilon-amine and in coordinating the methyl groups after transfer to facilitate multiple rounds of lysine methylation.

Selected figure(s)

Figure 1.
FIGURE 1. Structures of AdoMet, AdoHcy, and the cofactor analogs Sinefungin (adenosyl-L-ornithine) and AzaAdoMet.

Figure 6.
FIGURE 6. Proposed catalytic role of the methyl transfer pore in the SET domain active site. The carbonyl oxygens of Ser-221 and Asp-239 and the hydroxyl group of the invariant Tyr-287 engage in CH···O hydrogen bonding with the AdoMet methyl group, aligning it for the S[N]2 transfer to the lysine -amine.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 19280-19287) copyright 2006.

Figures were selected by an automated process.