Kinetic Mechanism of Protein Arginine Methyltransferase 1

Obianyo, Obiamaka; Osborne, Tanesha C.; Thompson, Paul R.

doi:10.1021/bi800904m

Cited by 71 publications

(108 citation statements)

References 37 publications

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“…1F), significantly exceeding the enzyme concentration of 10 nM, and production of di-methylated peptide could not be observed until the concentration of the monomethylated peptide exceeded that of the unmethylated substrate. This result demonstrates that PRMT5 has a nonprocessive enzymatic mechanism for peptide substrates, in contrast to the partially processive mechanism described for PRMT1 (36). Lack of processivity for the PRMT5 or PRMT5:MEP50 complex was observed at all tested concentrations of the peptide (0.01-10 μM) and AdoMet (0.1-10 μM).…”

Section: Resultsmentioning

confidence: 65%

Crystal structure of the human PRMT5:MEP50 complex

Antonysamy

Bonday

Campbell

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

285

385

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Protein arginine methyltransferases (PRMTs) play important roles in several cellular processes, including signaling, gene regulation, and transport of proteins and nucleic acids, to impact growth, differentiation, proliferation, and development. PRMT5 symmetrically di-methylates the two-terminal ω-guanidino nitrogens of arginine residues on substrate proteins. PRMT5 acts as part of a multimeric complex in concert with a variety of partner proteins that regulate its function and specificity. A core component of these complexes is the WD40 protein MEP50/WDR77/p44, which mediates interactions with binding partners and substrates. We have determined the crystal structure of human PRMT5 in complex with MEP50 (methylosome protein 50), bound to an S-adenosylmethionine analog and a peptide substrate derived from histone H4. The structure of the surprising hetero-octameric complex reveals the close interaction between the seven-bladed β-propeller MEP50 and the N-terminal domain of PRMT5, and delineates the structural elements of substrate recognition.epigenetics | protein-protein complex | A9145C P osttranslational methylation of lysine and arginine residues by protein lysine methyltransferases and protein arginine methyltransferases (PRMTs) alters the activity and interactions of substrate proteins, with crucial consequences to diverse cellular functions (1-3). Histone methylation is an epigenetic mark that plays a vital role in normal cell function, and whose dysregulation is associated with several diseases (4).The PRMT family of methyltransferases belongs to the largest class (class I) of S-adenosylmethionine (AdoMet)-dependent methyltransferase enzymes, responsible for the transfer of a methyl group from AdoMet to the arginine side-chains of histones and other proteins. PRMTs are further subdivided into type I, type II, type III, and type IV enzymes based on their patterns of arginine methylation. Eleven human PRMTs have been identified to date (5), and they all methylate the terminal guanidino nitrogen atoms of arginine residues. Type I PRMT enzymes (PRMT1, -2, -3, -4, -6, and -8) generate ω-NG-monomethyl and ω-NG,NG-asymmetric di-methyl arginines, whereas PRMT5 is a type II PRMT that catalyzes the formation of ω-NG-monomethyl and ω-NG,N′G-symmetric di-methyl arginine residues. PRMT7 was initially thought to have type II activity, but recent evidence suggests that it may be a type III enzyme that is only able to monomethylate substrates to form ω-NG-monomethyl arginine (6). A type IV enzyme that catalyses the formation of δ-N-methyl arginine has been identified in yeast (7). All PRMTs share the highly conserved methyltransferase catalytic domain, and several PRMTs contain additional domains that modulate their activity and specificity. PRMT2, PRMT3, and PRMT9 contain SH3, zinc finger, and TRP2 domains, respectively, and PRMT5 contains a largely uncharacterized N-terminal region.In contrast to type I PRMTs, PRMT5 functions as part of various high molecular weight protein complexes that invariably contain the WD-repe...

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Section: Resultsmentioning

confidence: 65%

Crystal structure of the human PRMT5:MEP50 complex

Antonysamy

Bonday

Campbell

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

285

385

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“…Several experimental studies have been performed to address this question. [27][28][29][30] For Type I enzymes, it was proposed that the active site methionine residues might prevent the binding of -MMA in a conformation that allows the formation of symmetric product. For Type II enzymes, this position is occupied by the residues with smaller side chains, such as Ser as observed in PRMT5.…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies also suggested that -MMA formation was not obligatory. 27 -MMA might be further methylated to form ADMA before being released from the active site. These results along with the previous suggestion that both methyl groups were added to the N 2 atom explain why the asymmetric product is formed from the PRMT3-catalyzed reaction.…”

Section: First and Second Methylations On The N 2 Atommentioning

confidence: 99%

QM/MM MD and free energy simulations of the methylation reactions catalyzed by protein arginine methyltransferase PRMT3

Chu

Guo

2013

Can. J. Chem.

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Protein arginine N-methyltransferases (PRMTs) catalyze the transfer of methyl group(s) from S-adenosyl-L-methionine (AdoMet) to the guanidine group of arginine residue in abundant eukaryotic proteins. Two major types of PRMTs have been identified in mammalian cells. Type I PRMTs catalyze the formation of asymmetric -N G , N G -dimethylarginine (ADMA), while Type II PRMTs catalyze the formation of symmetric -N G , N= G -dimethylarginine (SDMA). The two different methylation products (ADMA or SDMA) of the substrate could lead to different biological consequences. Although PRMTs have been the subject of extensive experimental investigations, the origin of the product specificity remains unclear. In this study, quantum mechanical/ molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations are performed to study the reaction mechanism for one of Type I PRMTs, PRMT3, and to gain insights into the energetic origin of its product specificity (ADMA). Our simulations have identified some important interactions and proton transfers involving the active site residues. These interactions and proton transfers seem to be responsible, at least in part, in making the N 2 atom of the substrate arginine the target of the both 1st and 2nd methylations, leading to the asymmetric dimethylation product. The simulations also suggest that the methyl transfer and proton transfer appear to be somehow concerted processes and that Glu326 is likely to function as the general base during the catalysis.Key words: protein arginine methyltransferases, product specificity, QM/MM, MD and free energy simulations, reaction mechanism.Résumé : Les protéines arginine N-méthyltransférases (PRMT) catalysent le transfert d'un ou de plusieurs groupes méthyle de la S-adénosyl-L-méthionine (AdoMet) au groupe guanidine du résidu arginine dans les protéines abondantes chez les eucaryotes. Deux types importants de PRMT ont été identifiés dans les cellules des mammifères. Les PRMT de type I catalysent la formation de -N G , N G -diméthylarginine asymétrique (DMAA), tandis que les PRMT de type II catalysent la formation de -N G , N= G -diméthylarginine symétrique (DMAS). Les conséquences biologiques de ces deux produits de méthylation distincts (DMAA ou DMAS) du substrat pourraient différer. Alors que les PRMT ont fait l'objet d'études expérimentales approfondies, l'origine de la spécificité du produit demeure obscure. Dans la présente étude, on procède à des simulations de dynamique moléculaire (DM) et d'énergies libres par des méthodes de mécanique quantique/mécanique moléculaire (MQ/MM) afin d'étudier le mécanisme de réaction pour l'une des PRMT de type I, la PMRT3, et de dégager des indices quant à l'origine énergétique de la spécificité de son produit (DMAA). Nos simulations ont permis d'identifier certaines interactions et certains transferts de proton importants faisant intervenir les résidus aux sites actifs. Ces interactions et transferts de protons semblent être responsables, du moins en partie, du fait que l'atome N 2 du...

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“…These peptides are used as substrates of PRMT1 and PRMT5 to evaluate how different acetylation combinations affect the methylation of Arg-3 catalyzed by these two enzymes. It is worthwhile to stress that our data and others have fully determined that the N-terminal H4 peptide sequence represents an authentic substrate of PRMT1, and its catalytic properties are very similar to that of the full-length H4 protein (50). All the peptides were synthesized using the standard Fmoc SPPS protocols, purified on C-18 reversed phase HPLC column, and confirmed with MALDI-MS as described previously (51).…”

Section: Design Synthesis and Characterization Of Modified H4mentioning

confidence: 93%

Histone H4 Acetylation Differentially Modulates Arginine Methylation by an in Cis Mechanism

Feng

Wang²,

Asher

et al. 2011

Journal of Biological Chemistry

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Histone H4 undergoes extensive post-translational modifications (PTMs) at its N-terminal tail. Many of these PTMs profoundly affect the on and off status of gene transcription. The molecular mechanism by which histone PTMs modulate genetic and epigenetic processes is not fully understood. In particular, how a PTM mark affects the presence and level of other histone modification marks needs to be addressed and is essential for better understanding the molecular basis of histone code hypothesis. To dissect the interplaying relationship between different histone modification marks, we investigated how individual lysine acetylations and their different combinations at the H4 tail affect Arg-3 methylation in cis. Our data reveal that the effect of lysine acetylation on arginine methylation depends on the site of acetylation and the type of methylation. Although certain acetylations present a repressive impact on PRMT1-mediated methylation (type I methylation), lysine acetylation generally is correlated with enhanced methylation by PRMT5 (type II dimethylation). In particular, Lys-5 acetylation decreases the activity of PRMT1 but increases that of PRMT5. Furthermore, circular dichroism study and computer simulation demonstrate that hyperacetylation increases the content of ordered secondary structures at the H4 tail region. These findings provide new insights into the regulatory mechanism of Arg-3 methylation by H4 acetylation and unravel the complex intercommunications that exist between different the PTM marks in cis. The divergent activities of PRMT1 and PRMT5 with respect to different acetyl-H4 substrates suggest that type I and type II proteinarginine methyltransferases use distinct molecular determinants for substrate recognition and catalysis.

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Kinetic Mechanism of Protein Arginine Methyltransferase 1

Cited by 71 publications

References 37 publications

Crystal structure of the human PRMT5:MEP50 complex

Crystal structure of the human PRMT5:MEP50 complex

QM/MM MD and free energy simulations of the methylation reactions catalyzed by protein arginine methyltransferase PRMT3

Histone H4 Acetylation Differentially Modulates Arginine Methylation by an in Cis Mechanism

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