1UMY

BHMT from rat liver


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 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

  • 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 h ...

    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: 
    • 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.,Sect.D 58: 1507
    • 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


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Betaine--homocysteine S-methyltransferase 1
A, B, C, D
407Rattus norvegicusMutation(s): 0 
Gene Names: Bhmt
EC: 2.1.1.5
Find proteins for O09171 (Rattus norvegicus)
Go to UniProtKB:  O09171
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.830α = 90.00
b = 149.270β = 92.92
c = 96.250γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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