PDBsum entry 1nth

Transferase

PDB id: 1nth

Contents

Protein chain

457 a.a.

Waters ×463

PDB id:

1nth

Name:

Transferase

Title:

Crystal structure of the methanosarcina barkeri monomethylamine methyltransferase (mtmb)

Structure:

Monomethylamine methyltransferase mtmb1. Chain: a. Synonym: mma methyltransferase 1, mmamt 1. Ec: 2.1.1.-

Source:

Methanosarcina barkeri. Organism_taxid: 2208. Strain: ms

Biol. unit:

Hexamer (from PDB file)

Resolution:

1.55Å R-factor: 0.176 R-free: 0.188

Authors:

B.Hao,W.Gong,T.K.Ferguson,C.M.James,J.A.Krzycki,M.K.Chan

Key ref:

B.Hao et al. (2002). A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science, 296, 1462-1466. PubMed id: 12029132 DOI: 10.1126/science.1069556

Date:

30-Jan-03 Release date: 04-Feb-03

Supersedes:

1l2r

Protein chain

O30642  (MTMB1_METBA) -  Monomethylamine methyltransferase MtmB1 from Methanosarcina barkeri

Seq: 458 a.a.

Struc: 457 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.1.1.248 - [methylamine--corrinoid protein] Co-methyltransferase.
• Reaction: Co(I)-[methylamine-specific corrinoid protein] + methylamine + H⁺ = methyl-Co(III)-[methylamine-specific corrinoid protein] + NH4⁺

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

Key reference

DOI no: 10.1126/science.1069556

Science 296:1462-1466 (2002)

PubMed id: 12029132

A new UAG-encoded residue in the structure of a methanogen methyltransferase.

B.Hao, W.Gong, T.K.Ferguson, C.M.James, J.A.Krzycki, M.K.Chan.

ABSTRACT

Genes encoding methanogenic methylamine methyltransferases all contain an in-frame amber (UAG) codon that is read through during translation. We have identified the UAG-encoded residue in a 1.55 angstrom resolution structure of the Methanosarcina barkeri monomethylamine methyltransferase (MtmB). This structure reveals a homohexamer comprised of individual subunits with a TIM barrel fold. The electron density for the UAG-encoded residue is distinct from any of the 21 natural amino acids. Instead it appears consistent with a lysine in amide-linkage to (4R,5R)-4-substituted-pyrroline-5-carboxylate. We suggest that this amino acid be named l-pyrrolysine.

Selected figure(s)

Figure 2.
Fig. 2. (A) Fit of (4R,5R)-4-substituted-pyrroline-5-carboxylate to the 2F[O] - F[C] 3 density of the NaCl crystal form (orientation 1). The substituent attached to the C-4 carbon is shown as a methyl, but it could also be an ammonium or hydroxyl group. (B) Stick-diagram of proposed L-pyrrolysine amino acid. (C) Residual F[O] - F[C] difference map of NH[4]SO[4] crystal form after incorporation of a 40% occupancy model consisting of L-pyrrolysine in orientation 1 and an exogenous ammonium ion. This remaining omit density suggests that L-pyrrolysine adopts a different orientation (orientation 2) at 60% occupancy in NH[4]SO[4] with an amine added to the C-2 carbon of the pyrroline ring. These figures were prepared with the programs XtalView, MOLSCRIPT, and Raster3D (22-24).

Figure 3.
Fig. 3. Stereoview of primary forms of the active site around the amber-encoded ligand: (A) NaCl crystals; (B) (NH[4])[2]SO[4] crystals, 40% occupancy orientation that is similar to NaCl crystals; (C) (NH[4])[2]SO[4] crystals, 60% occupancy orientation with amine added to ring. These figures were prepared with the programs XtalView, MOLSCRIPT, and Raster3D. (22-24).

The above figures are reprinted by permission from the AAAs: Science (2002, 296, 1462-1466) copyright 2002.

Figures were selected by the author.

Author's comment

It is now known that the substituent at the 4-position on the pyrroline ring is a methyl group and hence the molecule in Fig. 2 is a (4R,5R)-4-methyl-pyrroline-5-carboxylate. See Hao et el (2004). Reactivity and chemical synthesis of L-pyrrolysine- the 22(nd) genetically encoded amino acid. Chem Biol., 11, 1317-24.
L-pyrrolysine, the 22(nd) genetically encoded amino acid, was previously deduced to be (4R, 5R)-4-substituted-pyrroline-5-carboxylate attached to the epsilon-nitrogen of lysine based on the crystal structure of the M. barkeri monomethylamine methyltransferase (MtmB). To confirm L-pyrrolysine's identity, structures of MtmB have been determined following treatment with hydroxylamine, N-methylhydroxylamine, or dithionite. Analysis of these structures has provided additional support for the presence of the pyrroline ring and, together with previous mass spectroscopy data, has led us to assign the C(4)-substituent to a methyl group. Based on this assignment, synthetic L-pyrrolysine was prepared by chemical methods. Detailed study of this chemically synthesized L-pyrrolysine has allowed us to characterize its physical properties, to study its chemical stability, and to elucidate the role of its C(4) substituent. Future applications of this synthetic L-pyrrolysine include its in vivo incorporation into recombinant proteins.
Michael Chan, Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA.