PROSITE documentation PDOC51562
mRNA cap 0 methyltransferase domain profile


Most mRNAs undergo a chemical modification called capping resulting in a cap at the 5' end of the newly transcribed mRNA. The 5' cap 0 structure consists of a guanine nucleotide methylated at position 7 connected to the mRNA's initiating nucleoside via an inverted 5'-5' triphosphate linkage. After formation of the 5' cap 0, the mRNA's first base usually goes through a methylation on the 2'-O position of its ribose resulting in the 5' cap 1 structure. Further methylations can occur on the first and second nucleotides leading to the 5' cap 2 structure [1,2,3].

The 5' cap structure is essential as it protects mRNA by preventing degradation by 5' exoribonucleases and it also promotes translation [1,2,3].

Before capping, the precursor (pre-) mRNA has three phosphate groups linked to the 5'carbon of its first nucleoside. Capping (here: formation of the 5' cap 0 structure only) calls for three consecutive reactions on the nascent pre-mRNA: 1. Removal by hydrolysis of the pre-mRNA's γ-phosphate by RNA 5' triphosphatase (EC [E1]. 2. Addition of GMP from GTP to the 5' diphosphate RNA by RNA guanylyltransferase (EC [E2]. 3. Methylation of the 5' GpppN by a cap-specific RNA (guanine-N7) methyltransferase (EC [E3]. The enzyme uses S-adenosylmethionine (AdoMet or SAM) as the methyl donor and leads to the formation of the m7GpppRNA structure (the 5' cap) and S-adenosylhomocysteine (AdoHcy) [1,2,3].

As the capping apparatus, formed by the protein(s) carrying out the three capping reactions, is specifically targeted to RNA polymerase II transcripts, capping concerns most eukaryotic cellular and viral eukaryotic mRNAs. Although the capping apparatus is functionally conserved in eukaryotes, it differs between organisms regarding subunit organization. In yeast, there is one enzyme per each catalytic activity while in metazoans and plants the triphosphatase and the guanylyltransferase are encoded by a single gene. In all eukaryotic organisms, the methyltransferase is encoded by a gene that only encodes this activity [1,2,3].

The 3D structure of the cap methyltransferase Ecm1 from the microsporidian parasite Encephalitozoon cuniculi has been determined bound to AdoMet, AdoHcy and the cap guanilate methyl acceptor (see <PDB:1RI1>). It is a small monomeric enzyme that contains virtually nothing more than the catalytic domain. The protein contains 9 α helices and 11 β strands and altogether displays a rossmanoidal fold characteristic of Class I SAM-binding methyltransferases (see <PDOC51555>). It also exhibits structural features that appear unique to mRNA (guanine-N(7)-)-methyltransferases (mRNA-Cap0-MTs hereafter) such as a N-terminal region comprising about 40 amino acids that are disordered in the crystals, among which amino acids 30 to 40, not visible in the crystal structure, happen to be essential for Ecm1 activity [1]. The structure of Ecm1 can be divided up into two segments in-between which a large cleft with two ligand binding pockets results. This cleft contains solvent exposed amino acids that are conserved among other mRNA-Cap0-MTs. The second segment contains the elements associated with AdoMet binding in other Class I MTs and when AdoMet is bound to Ecm1, this segments forms a pocket that AdoMet expectedly occupies. When co-crystallized with Ecm1, the cap analog m7GpppG is bound in a pocket adjacent to the one binding AdoMet. Catalysis seems not to be operated through direct involvement of specific amino acid side chains, since no residue is observed to be in direct contact with the guanosine-N7 nucleophile, nor the the AdoMet methyl carbon nor the AdoHcy sulfur leaving group. Instead, Ecm1 manifestly ease methyl transfer to the cap guanine-N7 by coordinating the different players in an environment that optimizes substrate proximity and orientation [1].

Several eukaryotic DNA and RNA viruses encode some or all the capping enzymatic activities, often on a single polypeptide. As such, the vaccinia virus, a poxvirus used in vaccination against smallpox, encodes for two polypeptides responsible for mRNA capping: D1 and D12. D1 contains an N-terminal domain responsible for the triphosphatase and the guanylyltransferase activities and a C-terminal region containing the mRNA-Cap0-MT domain. In order for the mRNA-Cap0-MT domain of D1 to be fully active, D1 needs to associate with D12, a stimulatory subunit [2].

The crystal structure of the mRNA-Cap0-MT domain of the vaccinia virus D1 bound to AdoHcy in complex with its stimulatory D12 subunit has also been described (see <PDB:2VDW>). All in all, the vaccinia mRNA-Cap0-MT domain shows a conformation that is quite similar to the one of Ecm1, except for one difference: the N-terminal extension of the vaccinia domain folds back over the AdoHcy binding site, burying the ligand; this N-terminal section is involved catalytically as several amino acids in it bind AdoHcy [1,2].

The profile we developed covers the entire mRNA-Cap0-MT domain.

Last update:

November 2022 / Profile revised.


Technical section

PROSITE method (with tools and information) covered by this documentation:

RNA_CAP0_MT, PS51562; mRNA (guanine-N(7)-)-methyltransferase (EC domain profile  (MATRIX)


1AuthorsFabrega C. Hausmann S. Shen V. Shuman S. Lima C.D.
TitleStructure and mechanism of mRNA cap (guanine-N7) methyltransferase.
SourceMol. Cell 13:77-89(2004).
PubMed ID14731396

2AuthorsDe la Pena M. Kyrieleis O.J. Cusack S.
TitleStructural insights into the mechanism and evolution of the vaccinia virus mRNA cap N7 methyl-transferase.
SourceEMBO J. 26:4913-4925(2007).
PubMed ID17989694

3AuthorsBenarroch D. Smith P. Shuman S.
TitleCharacterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain.
SourceStructure 16:501-512(2008).
PubMed ID18400173




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