5L8X

X-RAY STRUCTURE OF APO METHANOCALDOCOCCUS JANNASCHII METHYLTRANSFERASE SUBUNIT A AT 1.85 ANGSTROM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

MtrA of the sodium ion pumping methyltransferase binds cobalamin in a unique mode.

Wagner, T.Ermler, U.Shima, S.

(2016) Sci Rep 6: 28226-28226

  • DOI: 10.1038/srep28226
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the three domains of life, vitamin B12 (cobalamin) is primarily used in methyltransferase and isomerase reactions. The methyltransferase complex MtrA-H of methanogenic archaea has a key function in energy conservation by catalysing the methyl tran ...

    In the three domains of life, vitamin B12 (cobalamin) is primarily used in methyltransferase and isomerase reactions. The methyltransferase complex MtrA-H of methanogenic archaea has a key function in energy conservation by catalysing the methyl transfer from methyl-tetrahydromethanopterin to coenzyme M and its coupling with sodium-ion translocation. The cobalamin-binding subunit MtrA is not homologous to any known B12-binding proteins and is proposed as the motor of the sodium-ion pump. Here, we present crystal structures of the soluble domain of the membrane-associated MtrA from Methanocaldococcus jannaschii and the cytoplasmic MtrA homologue/cobalamin complex from Methanothermus fervidus. The MtrA fold corresponds to the Rossmann-type α/β fold, which is also found in many cobalamin-containing proteins. Surprisingly, the cobalamin-binding site of MtrA differed greatly from all the other cobalamin-binding sites. Nevertheless, the hydrogen-bond linkage at the lower axial-ligand site of cobalt was equivalently constructed to that found in other methyltransferases and mutases. A distinct polypeptide segment fixed through the hydrogen-bond linkage in the relaxed Co(III) state might be involved in propagating the energy released upon corrinoid demethylation to the sodium-translocation site by a conformational change.


    Organizational Affiliation

    PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, 332-0012 Saitama, Japan.,Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany.,Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tetrahydromethanopterin S-methyltransferase subunit A
A
172Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: mtrA
EC: 2.1.1.86
Find proteins for Q58261 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58261
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tetrahydromethanopterin S-methyltransferase subunit A
B
173Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: mtrA
EC: 2.1.1.86
Find proteins for Q58261 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58261
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLT
Query on MLT

Download SDF File 
Download CCD File 
B
D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
LMR
Query on LMR

Download SDF File 
Download CCD File 
A
(2S)-2-hydroxybutanedioic acid
L-Malate
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.690α = 90.00
b = 37.030β = 91.98
c = 65.160γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
MOLREPphasing
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and technology agency (JST)JapanPRESTO

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-07-06
    Type: Database references