1Q8J

Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+, Hcy, methyltetrahydrofolate complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase.

Evans, J.C.Huddler, D.P.Hilgers, M.T.Romanchuk, G.Matthews, R.G.Ludwig, M.L.

(2004) Proc.Natl.Acad.Sci.Usa 101: 3729-3736

  • DOI: 10.1073/pnas.0308082100
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • B(12)-dependent methionine synthase (MetH) is a large modular enzyme that utilizes the cobalamin cofactor as a methyl donor or acceptor in three separate reactions. Each methyl transfer occurs at a different substrate-binding domain and requires a di ...

    B(12)-dependent methionine synthase (MetH) is a large modular enzyme that utilizes the cobalamin cofactor as a methyl donor or acceptor in three separate reactions. Each methyl transfer occurs at a different substrate-binding domain and requires a different arrangement of modules. In the catalytic cycle, the cobalamin-binding domain carries methylcobalamin to the homocysteine (Hcy) domain to form methionine and returns cob(I)alamin to the folate (Fol) domain for remethylation by methyltetrahydrofolate (CH(3)-H(4)folate). Here, we describe crystal structures of a fragment of MetH from Thermotoga maritima comprising the domains that bind Hcy and CH(3)-H(4)folate. These substrate-binding domains are (beta alpha)(8) barrels packed tightly against one another with their barrel axes perpendicular. The properties of the domain interface suggest that the two barrels remain associated during catalysis. The Hcy and CH(3)-H(4)folate substrates are bound at the C termini of their respective barrels in orientations that position them for reaction with cobalamin, but the two active sites are separated by approximately 50 A. To complete the catalytic cycle, the cobalamin-binding domain must travel back and forth between these distant active sites.


    Organizational Affiliation

    Department of Biological Chemistry and Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-methyltetrahydrofolate S-homocysteine methyltransferase
A, B
566Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Find proteins for Q9WYA5 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WYA5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2F
Query on C2F

Download SDF File 
Download CCD File 
A, B
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
C20 H25 N7 O6
ZNOVTXRBGFNYRX-STQMWFEESA-N
 Ligand Interaction
HCS
Query on HCS

Download SDF File 
Download CCD File 
A, B
2-AMINO-4-MERCAPTO-BUTYRIC ACID
C4 H9 N O2 S
FFFHZYDWPBMWHY-VKHMYHEASA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.980α = 90.00
b = 86.070β = 100.30
c = 125.820γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
XDSdata scaling
XDSdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description