Oxidized Homo sapiens betaine-homocysteine S-methyltransferase in complex with four Sm(III) ions

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Betaine-homocysteine methyltransferase: zinc in a distorted barrel.

Evans, J.C.Huddler, D.P.Jiracek, J.Castro, C.Millian, N.S.Garrow, T.A.Ludwig, M.L.

(2002) Structure 10: 1159-1171

  • DOI: https://doi.org/10.1016/s0969-2126(02)00796-7
  • Primary Citation of Related Structures:  
    1LT7, 1LT8

  • PubMed Abstract: 

    Betaine-homocysteine methyl transferase (BHMT) catalyzes the synthesis of methionine from betaine and homocysteine (Hcy), utilizing a zinc ion to activate Hcy. BHMT is a key liver enzyme that is important for homocysteine homeostasis. X-ray structures of human BHMT in its oxidized (Zn-free) and reduced (Zn-replete) forms, the latter in complex with the bisubstrate analog, S(delta-carboxybutyl)-L-homocysteine, were determined at resolutions of 2.15 A and 2.05 A. BHMT is a (beta/alpha)(8) barrel that is distorted to construct the substrate and metal binding sites. The zinc binding sequences G-V/L-N-C and G-G-C-C are at the C termini of strands beta6 and beta8. Oxidation to the Cys217-Cys299 disulfide and expulsion of Zn are accompanied by local rearrangements. The structures identify Hcy binding fingerprints and provide a prototype for the homocysteine S-methyltransferase family.

  • Organizational Affiliation

    Biophysics Research Division and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
406Homo sapiensMutation(s): 6 
UniProt & NIH Common Fund Data Resources
Find proteins for Q93088 (Homo sapiens)
Explore Q93088 
Go to UniProtKB:  Q93088
PHAROS:  Q93088
GTEx:  ENSG00000145692 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93088
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.99α = 90
b = 90.085β = 122.1
c = 89.085γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations