Molecular basis of the reaction mechanism of the methyltransferase HENMT1
(2024) In PLoS ONE 19(1).- Abstract
PIWI-interacting RNAs (piRNAs) are important for ensuring the integrity of the germline. 3'-terminal 2'-O-methylation is essential for piRNA maturation and to protect them from degradation. HENMT1 (HEN Methyltransferase 1) carries out the 2'-O-methylation, which is of key importance for piRNA stability and functionality. However, neither the structure nor the catalytic mechanism of mammalian HENMT1 have been studied. We have constructed a catalytic-competent HENMT1 complex using computational approaches, in which Mg2+ is primarily coordinated by four evolutionary conserved residues, and is further auxiliary coordinated by the 3'-O and 2'-O on the 3'-terminal nucleotide of the piRNA. Our study suggests that metal has limited effects on... (More)
PIWI-interacting RNAs (piRNAs) are important for ensuring the integrity of the germline. 3'-terminal 2'-O-methylation is essential for piRNA maturation and to protect them from degradation. HENMT1 (HEN Methyltransferase 1) carries out the 2'-O-methylation, which is of key importance for piRNA stability and functionality. However, neither the structure nor the catalytic mechanism of mammalian HENMT1 have been studied. We have constructed a catalytic-competent HENMT1 complex using computational approaches, in which Mg2+ is primarily coordinated by four evolutionary conserved residues, and is further auxiliary coordinated by the 3'-O and 2'-O on the 3'-terminal nucleotide of the piRNA. Our study suggests that metal has limited effects on substrate and cofactor binding but is essential for catalysis. The reaction consists of deprotonation of the 2'-OH to 2'-O and a methyl transfer from SAM to the 2'-O. The methyl transfer is spontaneous and fast. Our in-depth analysis suggests that the 2'-OH may be deprotonated before entering the active site or it may be partially deprotonated at the active site by His800 and Asp859, which are in a special alignment that facilitates the proton transfer out of the active site. Furthermore, we have developed a detailed potential reaction scenario indicating that HENMT1 is Mg2+ utilizing but is not a Mg2+ dependent enzyme.
(Less)
- author
- Kaldis, Philipp LU and Zhao, Li Na LU
- organization
- publishing date
- 2024-01-10
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS ONE
- volume
- 19
- issue
- 1
- article number
- e0293243
- pages
- 17 pages
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- scopus:85182096692
- pmid:38198468
- ISSN
- 1932-6203
- DOI
- 10.1371/journal.pone.0293243
- language
- English
- LU publication?
- yes
- additional info
- Copyright: © 2024 Kaldis, Zhao. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
- id
- f58e33ab-e24b-4072-9b85-10f156c2ca58
- date added to LUP
- 2024-01-11 14:19:59
- date last changed
- 2024-04-19 04:47:02
@article{f58e33ab-e24b-4072-9b85-10f156c2ca58, abstract = {{<p>PIWI-interacting RNAs (piRNAs) are important for ensuring the integrity of the germline. 3'-terminal 2'-O-methylation is essential for piRNA maturation and to protect them from degradation. HENMT1 (HEN Methyltransferase 1) carries out the 2'-O-methylation, which is of key importance for piRNA stability and functionality. However, neither the structure nor the catalytic mechanism of mammalian HENMT1 have been studied. We have constructed a catalytic-competent HENMT1 complex using computational approaches, in which Mg2+ is primarily coordinated by four evolutionary conserved residues, and is further auxiliary coordinated by the 3'-O and 2'-O on the 3'-terminal nucleotide of the piRNA. Our study suggests that metal has limited effects on substrate and cofactor binding but is essential for catalysis. The reaction consists of deprotonation of the 2'-OH to 2'-O and a methyl transfer from SAM to the 2'-O. The methyl transfer is spontaneous and fast. Our in-depth analysis suggests that the 2'-OH may be deprotonated before entering the active site or it may be partially deprotonated at the active site by His800 and Asp859, which are in a special alignment that facilitates the proton transfer out of the active site. Furthermore, we have developed a detailed potential reaction scenario indicating that HENMT1 is Mg2+ utilizing but is not a Mg2+ dependent enzyme.</p>}}, author = {{Kaldis, Philipp and Zhao, Li Na}}, issn = {{1932-6203}}, language = {{eng}}, month = {{01}}, number = {{1}}, publisher = {{Public Library of Science (PLoS)}}, series = {{PLoS ONE}}, title = {{Molecular basis of the reaction mechanism of the methyltransferase HENMT1}}, url = {{http://dx.doi.org/10.1371/journal.pone.0293243}}, doi = {{10.1371/journal.pone.0293243}}, volume = {{19}}, year = {{2024}}, }