PDBsum entry 2i2x

Transferase

PDB id: 2i2x

Contents

Protein chains

(+ 2 more) 459 a.a. *

(+ 2 more) 258 a.a. *

Ligands

B13 ×8

Metals

__K ×8

_ZN ×12

Waters ×946

* Residue conservation analysis

PDB id:

2i2x

Name:

Transferase

Title:

Crystal structure of methanol:cobalamin methyltransferase complex mtabc from methanosarcina barkeri

Structure:

Methyltransferase 1. Chain: a, c, e, g, i, k, m, o. Synonym: mtab. Methyltransferase 1. Chain: b, d, f, h, j, l, n, p. Synonym: mtac. Ec: 2.1.1.90

Source:

Methanosarcina barkeri. Organism_taxid: 2208. Strain: fuaro (dsm 804). Strain: fuaro (dsm 804)

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.184 R-free: 0.231

Authors:

C.H.Hagemeier,M.Kruer,R.K.Thauer,E.Warkentin,U.Ermler

Key ref:

C.H.Hagemeier et al. (2006). Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-cobalamin methyltransferase complex. Proc Natl Acad Sci U S A, 103, 18917-18922. PubMed id: 17142327 DOI: 10.1073/pnas.0603650103

Date:

17-Aug-06 Release date: 21-Nov-06

Protein chains

Q46EH3  (MTAB_METBF) -  Methanol--corrinoid protein co-methyltransferase from Methanosarcina barkeri (strain Fusaro / DSM 804)

Seq: 461 a.a.

Struc: 459 a.a.

Protein chains

Q46EH4  (MTAC_METBF) -  Methanol--corrinoid protein from Methanosarcina barkeri (strain Fusaro / DSM 804)

Seq: 258 a.a.

Struc: 258 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.2.1.1.90 - methanol--corrinoid protein Co-methyltransferase.
• Reaction: Co(I)-[methanol-specific corrinoid protein] + methanol + H⁺ = methyl- Co(III)-[methanol-specific corrinoid protein] + H2O

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

Key reference

DOI no: 10.1073/pnas.0603650103

Proc Natl Acad Sci U S A 103:18917-18922 (2006)

PubMed id: 17142327

Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-cobalamin methyltransferase complex.

C.H.Hagemeier, M.Krer, R.K.Thauer, E.Warkentin, U.Ermler.

ABSTRACT

Some methanogenic and acetogenic microorganisms have the catalytic capability to cleave heterolytically the C O bond of methanol. To obtain insight into the elusive enzymatic mechanism of this challenging chemical reaction we have investigated the methanol-activating MtaBC complex from Methanosarcina barkeri composed of the zinc-containing MtaB and the 5-hydroxybenzimidazolylcobamide-carrying MtaC subunits. Here we report the 2.5-A crystal structure of this complex organized as a (MtaBC)(2) heterotetramer. MtaB folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at the bottom of a funnel formed at the C-terminal beta-barrel end and ligates to two cysteinyl sulfurs (Cys-220 and Cys-269) and one carboxylate oxygen (Glu-164). MtaC is structurally related to the cobalamin-binding domain of methionine synthase. Its corrinoid cofactor at the top of the Rossmann domain reaches deeply into the funnel of MtaB, defining a region between zinc(II) and the corrinoid cobalt that must be the binding site for methanol. The active site geometry supports a S(N)2 reaction mechanism, in which the C O bond in methanol is activated by the strong electrophile zinc(II) and cleaved because of an attack of the supernucleophile cob(I)amide. The environment of zinc(II) is characterized by an acidic cluster that increases the charge density on the zinc(II), polarizes methanol, and disfavors deprotonation of the methanol hydroxyl group. Implications of the MtaBC structure for the second step of the reaction, in which the methyl group is transferred to coenzyme M, are discussed.

Selected figure(s)

Figure 1.
The MtaBC structure. (A) In the (MtaBC)[2] heterotetramer (in stereo) each MtaBC unit (MtaB in blue and MtaC in red) is related to its partner unit (in light blue and red) by a twofold noncrystallographic axis. The (MtaBC)[2] complex has a size of 62 Å × 55 Å × 52 Å and forms two active sites separated by a distance of 38 Å. The corrinoids are shown as stick models, and the zinc(II) ions are depicted by green spheres. The contact loops between the two active sites are highlighted in black. For oligomeric assembly the interactions between the N-terminal extension of MtaC (in green) and the counter MtaB are essential. (B) In the MtaBC unit the Rossmann domain (orange) of MtaC is only loosely associated with its helical domain (red) and MtaB (blue). MtaB is subdivided into a TIM barrel core (dark blue) and a helical layer (light blue). The active site is located between the corrinoid cobalt and zinc(II).

Figure 3.
Proposed mechanism of methanol activation. (A) Scheme of a unique acidic cluster that flanks the zinc and methanol-binding site. The acidic residues (in red) might play a crucial role in polarizing zinc(II) and methanol. The unclear peak X was tentatively assigned as a potassium ion. Methanol is modeled into the protein, and its distance to the corrinoid Co is estimated based on the distance between the zinc(II) and methanol oxygen of 2 Å. (B) S[N]2 mechanism for the methylation of 5-hydroxybenzimidazolyl cob(I)amide with methanol. The methanol is activated by the strong electrophile zinc(II) and attacked by the supernucleophile cob(I)amide.

Figures were selected by an automated process.