Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 181.38 kDa 
• Atom Count: 12191 
• Modelled Residue Count: 1469 
• Deposited Residue Count: 1624 
• Unique protein chains: 1

4M3P

Betaine-Homocysteine S-Methyltransferase from Homo sapiens complexed with Homocysteine

• PDB DOI: 10.2210/pdb4M3P/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-06 Released: 2014-06-18 
• Deposition Author(s): Koutmos, M., Yamada, K., Mladkova, J., Paterova, J., Diamond, C.E., Tryon, K., Jungwirth, P., Garrow, T.A., Jiracek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.219 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Specific potassium ion interactions facilitate homocysteine binding to betaine-homocysteine S-methyltransferase.

Mladkova, J., Hladilkova, J., Diamond, C.E., Tryon, K., Yamada, K., Garrow, T.A., Jungwirth, P., Koutmos, M., Jiracek, J.

(2014) Proteins 82: 2552-2564

• PubMed: 24895213 
• DOI: 10.1002/prot.24619
• Primary Citation of Related Structures:  
  4M3P


• PubMed Abstract: 
  

Betaine-homocysteine S-methyltransferase (BHMT) is a zinc-dependent methyltransferase that uses betaine as the methyl donor for the remethylation of homocysteine to form methionine. This reaction supports S-adenosylmethionine biosynthesis, which is required for hundreds of methylation reactions in humans. Herein we report that BHMT is activated by potassium ions with an apparent K(M) for K⁺ of about 100 µM. The presence of potassium ions lowers the apparent K(M) of the enzyme for homocysteine, but it does not affect the apparent K(M) for betaine or the apparent k(cat) for either substrate. We employed molecular dynamics (MD) simulations to theoretically predict and protein crystallography to experimentally localize the binding site(s) for potassium ion(s). Simulations predicted that K⁺ ion would interact with residues Asp26 and/or Glu159. Our crystal structure of BHMT bound to homocysteine confirms these sites of interaction and reveals further contacts between K⁺ ion and BHMT residues Gly27, Gln72, Gln247, and Gly298. The potassium binding residues in BHMT partially overlap with the previously identified DGG (Asp26-Gly27-Gly28) fingerprint in the Pfam 02574 group of methyltransferases. Subsequent biochemical characterization of several site-specific BHMT mutants confirmed the results obtained by the MD simulations and crystallographic data. Together, the data herein indicate that the role of potassium ions in BHMT is structural and that potassium ion facilitates the specific binding of homocysteine to the active site of the enzyme.

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Organizational Affiliation: 

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Betaine--homocysteine S-methyltransferase 1	A, B, C, D	406	Homo sapiens	Mutation(s): 0  Gene Names: BHMT EC: 2.1.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q93088 (Homo sapiens) Explore Q93088  Go to UniProtKB:  Q93088
PHAROS:  Q93088

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRT	H [auth B], O [auth D]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
HCS	G [auth A], K [auth B], N [auth C], R [auth D]	2-AMINO-4-MERCAPTO-BUTYRIC ACID C4 H9 N O2 S FFFHZYDWPBMWHY-VKHMYHEASA-N
ZN	E [auth A], I [auth B], L [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	F [auth A], J [auth B], M [auth C], Q [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.219 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.097	α = 90
b = 102.617	β = 101.76
c = 96.228	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
EPMR	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-06 
• Released Date: 2014-06-18 
Deposition Author(s): Koutmos, M., Yamada, K., Mladkova, J., Paterova, J., Diamond, C.E., Tryon, K., Jungwirth, P., Garrow, T.A., Jiracek, J.

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2014-10-08
  Changes: Database references