2I2X

Crystal structure of methanol:cobalamin methyltransferase complex MtaBC from Methanosarcina barkeri


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2006) Proc.Natl.Acad.Sci.Usa 103: 18917-18922

  • DOI: 10.1073/pnas.0603650103

  • PubMed 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 me ...

    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.


    Organizational Affiliation

    Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methyltransferase 1
A, C, E, G, I, K, M, O
461Methanosarcina barkeri (strain Fusaro / DSM 804)Mutation(s): 0 
Gene Names: mtaB
EC: 2.1.1.90
Find proteins for Q46EH3 (Methanosarcina barkeri (strain Fusaro / DSM 804))
Go to UniProtKB:  Q46EH3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Methyltransferase 1
B, D, F, H, J, L, N, P
258Methanosarcina barkeri (strain Fusaro / DSM 804)Mutation(s): 0 
Gene Names: mtaC
Find proteins for Q46EH4 (Methanosarcina barkeri (strain Fusaro / DSM 804))
Go to UniProtKB:  Q46EH4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
B13
Query on B13

Download SDF File 
Download CCD File 
B, D, F, H, J, L, N, P
5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE
C60 H88 Co N13 O15 P
QJVWXASLTDBQFK-LAYHTZHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 101.750α = 90.00
b = 172.850β = 98.86
c = 190.540γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACrefinement
ADSCdata collection
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-04-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Refinement description, Version format compliance