Methionine synthase, C-terminal fragment, Cobalamin and Reactivation Domains from Thermus thermophilus HB8

Experimental Data Snapshot

  • Resolution: 3.15 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.245 

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Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo.

Mendoza, J.Purchal, M.Yamada, K.Koutmos, M.

(2023) Nat Commun 14: 6365-6365

  • DOI: https://doi.org/10.1038/s41467-023-42037-4
  • Primary Citation of Related Structures:  
    8SSC, 8SSD, 8SSE

  • PubMed Abstract: 

    Cobalamin-dependent methionine synthase (MS) is a key enzyme in methionine and folate one-carbon metabolism. MS is a large multi-domain protein capable of binding and activating three substrates: homocysteine, folate, and S-adenosylmethionine for methylation. Achieving three chemically distinct methylations necessitates significant domain rearrangements to facilitate substrate access to the cobalamin cofactor at the right time. The distinct conformations required for each reaction have eluded structural characterization as its inherently dynamic nature renders structural studies difficult. Here, we use a thermophilic MS homolog (tMS) as a functional MS model. Its exceptional stability enabled characterization of MS in the absence of cobalamin, marking the only studies of a cobalamin-binding protein in its apoenzyme state. More importantly, we report the high-resolution full-length MS structure, ending a multi-decade quest. We also capture cobalamin loading in crystallo, providing structural insights into holoenzyme formation. Our work paves the way for unraveling how MS orchestrates large-scale domain rearrangements crucial for achieving challenging chemistries.

  • Organizational Affiliation

    Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine synthase
A, B, C, D, E
A, B, C, D, E, F
523Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA0618
Find proteins for Q5SKM5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKM5 
Go to UniProtKB:  Q5SKM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKM5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.15 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.245 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.135α = 90
b = 95.844β = 91.956
c = 238.745γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1945174

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Database references