PDBsum entry: 1p0y

Transferase

PDB id: 1p0y

Contents

Protein chains

430 a.a. *

Ligands

SAH ×3

MLZ ×3

Waters ×652

* Residue conservation analysis

PDB id:

1p0y

Name:

Transferase

Title:

Crystal structure of the set domain of lsmt bound to melysine and adohcy

Structure:

Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit n-methyltransferase, chloroplast. Chain: a, b, c. Synonym: [ribulose-bisphosphate-carboxylase]-lysine n- methyltransferase, rubisco methyltransferase, rubisco lsmt, rbcmt. Engineered: yes

Source:

Pisum sativum. Pea. Organism_taxid: 3888. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Trimer (from PQS)

Resolution:

2.55Å R-factor: 0.228 R-free: 0.269

Authors:

R.C.Trievel,E.M.Flynn,R.L.Houtz,J.H.Hurley

Key ref:

R.C.Trievel et al. (2003). Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT. Nat Struct Biol, 10, 545-552. PubMed id: 12819771 DOI: 10.1038/nsb946

Date:

11-Apr-03 Release date: 01-Jul-03

Protein chains

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

Seq: 489 a.a.

Struc: 430 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 = MLZ) matches with 62.00% similarity)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: chloroplast (1 term)
• Biochemical function: [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity (1 term)

reference

DOI no: 10.1038/nsb946

Nat Struct Biol 10:545-552 (2003)

PubMed id: 12819771

Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT.

R.C.Trievel, E.M.Flynn, R.L.Houtz, J.H.Hurley.

ABSTRACT

SET domain protein methyltransferases catalyze the transfer of methyl groups from the cofactor S-adenosylmethionine (AdoMet) to specific lysine residues of protein substrates, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex. The crystal structures of pea Rubisco large subunit methyltransferase (LSMT) in ternary complexes with either lysine or epsilon-N-methyllysine (MeLys) and the product S-adenosylhomocysteine (AdoHcy) were determined to resolutions of 2.65 and 2.55 A, respectively. The zeta-methyl group of MeLys is bound to the enzyme via carbon-oxygen hydrogen bonds that play a key role in catalysis. The methyl donor and acceptor are aligned in a linear geometry for S(N)2 nucleophilic transfer of the methyl group during catalysis. Differences in hydrogen bonding between the MeLys epsilon-amino group and Rubisco LSMT and SET7/9 explain why Rubisco LSMT generates multiply methylated Lys, wheras SET7/9 generates only MeLys.

Selected figure(s)

Figure 4.
Figure 4. Stereochemical mechanism of methyl group transfer. (a) Model of the lysine -AdoMet substrate complex on the basis of the LSMT SET -Lys -AdoHcy complex. The formation of the nascent bond between the deprotonated N of the lysine and the C methyl group of AdoMet is denoted with a dashed line, and the geometry of S[N]2 reaction is shown with a black arc. (b) Model of the MeLys -AdoMet substrate complex based on the LSMT SET -MeLys -AdoHcy complex. The figure is labeled as in a.

Figure 5.
Figure 5. Comparison of hydrogen bonding in the active sites of LSMT and SET7/9. (a) Stereo view of the superimposition of the lysine-binding clefts of LSMT (blue) and the SET7/9 -histone H3 MeLys4 -AdoHcy ternary complex (PDB entry 1O9S) (red). Hydrogen bonds between the protein and -amino groups, and carbon-oxygen hydrogen bonds between the invariant Tyr and methyl groups are illustrated with dashed magenta lines. (b) Stereo view of the superimposition of the lysine-binding clefts of LSMT (blue) and the SET7/9 -AdoMet complex (PDB entry 1N6A) (green). Hydrogen bonds are illustrated as in a.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 545-552) copyright 2003.

Figures were selected by the author.