1UMY

BHMT from rat liver


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of rat liver betaine homocysteine s-methyltransferase reveals new oligomerization features and conformational changes upon substrate binding.

Gonzalez, B.Pajares, M.A.Martinez-Ripoll, M.Blundell, T.L.Sanz-Aparicio, J.

(2004) J Mol Biol 338: 771-782

  • DOI: 10.1016/j.jmb.2004.03.005
  • Primary Citation of Related Structures:  
    1UMY

  • PubMed Abstract: 
  • Betaine homocysteine S-methyltransferase (BHMT) is one of the two enzymes known to methylate homocysteine to generate methionine in the liver. It presents a Zn(2+) atom linked to three essential Cys residues. The crystal structure of rat liver BHMT has been solved at 2 ...

    Betaine homocysteine S-methyltransferase (BHMT) is one of the two enzymes known to methylate homocysteine to generate methionine in the liver. It presents a Zn(2+) atom linked to three essential Cys residues. The crystal structure of rat liver BHMT has been solved at 2.5A resolution, using crystals with P2(1) symmetry and 45% solvent content in the cell. The asymmetric unit contains the whole functional tetramer showing point symmetry 222. The overall fold of the subunit consists mostly of a (alpha/beta)(8) barrel, as for human BHMT. From the end of the barrel, the polypeptide chain extends away and makes many interactions with a different subunit, forming tight dimers. The most remarkable structural feature of rat liver BHMT is the presence of a helix including residues 381-407, at the C terminus of the chain, which bind together the dimers AB to CD. A strong ion-pair and more than 60 hydrophobic interactions keep this helix stacked to the segment 316-349 from the opposite subunit. Moreover, the crystal structure of free rat liver BHMT clearly shows that Tyr160 is the fourth ligand coordinated to Zn, which is replaced by Hcy upon binding. Two residues essential for substrate recognition, Phe76 and Tyr77, are provided by a conformational change in a partially disordered loop (L2). The crucial role of these residues is highlighted by site-directed mutagenesis.


    Related Citations: 
    • Active-Site Mutagenesis Study of Rat Liver Betaine Homocysteine S-Methyltransferase
      Gonzalez, B., Garrido, F., Gasset, M., Sanz-Aparicio, J., Pajares, M.A.
      (2003) Biochem J 370: 945
    • Crystallization and Preliminary X-Ray Study of Recombinant Betaine-Homocysteine S-Methyltransferase from Rat Liver
      Gonzalez, B., Pajares, M.A., Too, P., Garrido, F., Blundell, T.L., Sanz-Aparicio, J.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 1507

    Organizational Affiliation

    Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Betaine--homocysteine S-methyltransferase 1A, B, C, D407Rattus norvegicusMutation(s): 0 
Gene Names: Bhmt
EC: 2.1.1.5
UniProt
Find proteins for O09171 (Rattus norvegicus)
Explore O09171 
Go to UniProtKB:  O09171
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.83α = 90
b = 149.27β = 92.92
c = 96.25γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-12-05
    Changes: Data collection, Database references, Source and taxonomy, Structure summary