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

Mládková, Jana ; Hladílková, Jana LU ; Diamond, Carrie E. ; Tryon, Katherine ; Yamada, Kazuhiro ; Garrow, Timothy A. ; Jungwirth, Pavel ; Koutmos, Markos and Jiráček, Jiří (2014) In Proteins: Structure, Function and Bioinformatics 82(10). p.2552-2564
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 KM for K+ of about 100 μM. The presence of potassium ions lowers the apparent KM of the enzyme for homocysteine, but it does not affect the apparent KM for betaine or the apparent kcat for either substrate. We employed molecular dynamics (MD) simulations to theoretically predict and protein crystallography... (More)

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 KM for K+ of about 100 μM. The presence of potassium ions lowers the apparent KM of the enzyme for homocysteine, but it does not affect the apparent KM for betaine or the apparent kcat 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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author
; ; ; ; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
BHMT, Crystal structure, Enzyme kinetics, Homocysteine, Molecular dynamics, Potassium, Simulations
in
Proteins: Structure, Function and Bioinformatics
volume
82
issue
10
pages
13 pages
publisher
John Wiley & Sons Inc.
external identifiers
  • scopus:84937731945
  • pmid:24895213
ISSN
0887-3585
DOI
10.1002/prot.24619
language
English
LU publication?
no
additional info
Publisher Copyright: © 2014 Wiley Periodicals, Inc.
id
8017c145-34e5-40cb-ba8e-bb4c0697ae0b
date added to LUP
2025-07-18 11:21:41
date last changed
2025-08-28 10:42:10
@article{8017c145-34e5-40cb-ba8e-bb4c0697ae0b,
  abstract     = {{<p>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<sub>M</sub> for K<sup>+</sup> of about 100 μM. The presence of potassium ions lowers the apparent K<sub>M</sub> of the enzyme for homocysteine, but it does not affect the apparent K<sub>M</sub> for betaine or the apparent k<sub>cat</sub> 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<sup>+</sup> 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<sup>+</sup> 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.</p>}},
  author       = {{Mládková, Jana and Hladílková, Jana and Diamond, Carrie E. and Tryon, Katherine and Yamada, Kazuhiro and Garrow, Timothy A. and Jungwirth, Pavel and Koutmos, Markos and Jiráček, Jiří}},
  issn         = {{0887-3585}},
  keywords     = {{BHMT; Crystal structure; Enzyme kinetics; Homocysteine; Molecular dynamics; Potassium; Simulations}},
  language     = {{eng}},
  number       = {{10}},
  pages        = {{2552--2564}},
  publisher    = {{John Wiley & Sons Inc.}},
  series       = {{Proteins: Structure, Function and Bioinformatics}},
  title        = {{Specific potassium ion interactions facilitate homocysteine binding to betaine-homocysteine <i>S</i>-methyltransferase}},
  url          = {{http://dx.doi.org/10.1002/prot.24619}},
  doi          = {{10.1002/prot.24619}},
  volume       = {{82}},
  year         = {{2014}},
}