PDBsum entry 1mlv

Transferase

PDB id: 1mlv

Contents

Protein chains

424 a.a. *

Ligands

SAH ×3

EPE ×3

Waters ×666

* Residue conservation analysis

PDB id:

1mlv

Name:

Transferase

Title:

Structure and catalytic mechanism of a set domain protein methyltransferase

Structure:

Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit n-methyltransferase. Chain: a, b, c. Fragment: residues 46-482. Synonym: [ribulose-biphosphate-carboxylase]-lysine n- methyltransferase, rubisco methyltransferase, rubisco lsmt, rbcmt. Engineered: yes

Source:

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

Biol. unit:

Hexamer (from PQS)

Resolution:

2.60Å R-factor: 0.232 R-free: 0.277

Authors:

R.C.Trievel,B.M.Beach,L.M.A.Dirk,R.L.Houtz,J.H.Hurley

Key ref:

R.C.Trievel et al. (2002). Structure and catalytic mechanism of a SET domain protein methyltransferase. Cell, 111, 91. PubMed id: 12372303 DOI: 10.1016/S0092-8674(02)01000-0

Date:

30-Aug-02 Release date: 30-Oct-02

Protein chains

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

Seq: 489 a.a.

Struc: 424 a.a.*

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

Enzyme reactions

• Enzyme class 1: E.C.2.1.1.127 - [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase.
• Reaction: L-lysyl-[ribulose-1,5-bisphosphate carboxylase] + 3 S-adenosyl-L- methionine = N₆,N₆,N₆-trimethyl-L-lysyl-[ribulose-1,5-bisphosphate carboxylase] + 3 S-adenosyl-L-homocysteine + 3 H⁺

L-lysyl-[ribulose-1,5-bisphosphate carboxylase] + 3 × S-adenosyl-L- methionine = N(6),N(6),N(6)-trimethyl-L-lysyl-[ribulose-1,5-bisphosphate carboxylase] + 3 × S-adenosyl-L-homocysteine + 3 × H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

• Enzyme class 2: E.C.2.1.1.259 - [fructose-bisphosphate aldolase]-lysine N-methyltransferase.
• Reaction: [fructose-bisphosphate aldolase]-L-lysine + 3 S-adenosyl-L-methionine = [fructose-bisphosphate aldolase]-N₆,N₆,N₆-trimethyl-L-lysine + 3 S-adenosyl-L-homocysteine + 3 H⁺

[fructose-bisphosphate aldolase]-L-lysine + 3 × S-adenosyl-L-methionine = [fructose-bisphosphate aldolase]-N(6),N(6),N(6)-trimethyl-L-lysine + 3 × S-adenosyl-L-homocysteine + 3 × H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/S0092-8674(02)01000-0

Cell 111:91 (2002)

PubMed id: 12372303

Structure and catalytic mechanism of a SET domain protein methyltransferase.

R.C.Trievel, B.M.Beach, L.M.Dirk, R.L.Houtz, J.H.Hurley.

ABSTRACT

Protein lysine methylation by SET domain enzymes regulates chromatin structure, gene silencing, transcriptional activation, plant metabolism, and other processes. The 2.6 A resolution structure of Rubisco large subunit methyltransferase in a pseudo-bisubstrate complex with S-adenosylhomocysteine and a HEPES ion reveals an all-beta architecture for the SET domain embedded within a larger alpha-helical enzyme fold. Conserved regions of the SET domain bind S-adenosylmethionine and substrate lysine at two sites connected by a pore. We propose that methyl transfer is catalyzed by a conserved Tyr at a narrow pore connecting the sites. The cofactor enters by a "back door" on the opposite side of the enzyme from substrate, promoting highly specific protein recognition and allowing addition of multiple methyl groups.

Selected figure(s)

Figure 1.
Figure 1. Structure of LSMT and the SET Domain

Figure 4.
Figure 4. Ligand Binding Sites

The above figures are reprinted by permission from Cell Press: Cell (2002, 111, 91-0) copyright 2002.

Figures were selected by the author.