4M3P

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

Summary for 4M3P

• Entry DOI: 10.2210/pdb4m3p/pdb
• Related: 1LT7 1LT8
• Descriptor: Betaine--homocysteine S-methyltransferase 1, ZINC ION, POTASSIUM ION, ... (6 entities in total)
• Functional Keywords: alpha and beta proteins (a/b), tim beta/alpha-barrel, methyltransferase activity, homocysteine s-methyltransferase activity, transferase activity, metal ion binding, betaine-homocysteine s-methyltransferase activity, protein complex binding, betaine, homocysteine, transferase
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: Q93088
• Total number of polymer chains: 4
• Total formula weight: 181380.46

Authors

Koutmos, M.,Yamada, K.,Mladkova, J.,Paterova, J.,Diamond, C.E.,Tryon, K.,Jungwirth, P.,Garrow, T.A.,Jiracek, J. (deposition date: 2013-08-06, release date: 2014-06-18, Last modification date: 2024-04-03)

Primary citation

Mladkova, J.,Hladilkova, J.,Diamond, C.E.,Tryon, K.,Yamada, K.,Garrow, T.A.,Jungwirth, P.,Koutmos, M.,Jiracek, J.
Specific potassium ion interactions facilitate homocysteine binding to betaine-homocysteine S-methyltransferase.
Proteins, 82:2552-2564, 2014

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.

PubMed: 24895213
DOI: 10.1002/prot.24619

Experimental method

X-RAY DIFFRACTION (1.895 Å)