Decapping complex

Dcp2, as the main catalyst of the decapping process, relies on a specific pattern of amino acids called a nudix domain to align itself with the 5' cap in order to hydrolyze it.^[5] A nudix domain is made by packing two beta sheets between multiple alpha helices, can be various lengths and sizes, and is generally used by proteins to carry out dephosphorylation, getting rid of a phosphate by inserting a water molecule into the bond between the phosphate and the rest of the molecule.^[10] In the case of Dcp2, it contains multiple glutamic acid side chains that are negatively charged in normal cellular conditions, and these are what allow the protein to manipulate water molecules to hydrolyze the tri-phosphate bridge that connects the 5' end of the mRNA to the 7-methylguanosine cap.^[5] Therefore, the nudix domain is what allows Dcp2 to remove the 5' cap, which results in the creation 7mGDP, a 7-methylguanosine with two phosphate groups attached, and a monophosphorylated mRNA strand.

Before the nudix domain is an N-terminal regulatory domain (NRD), which further helps hydrolyze the 5' mRNA cap. After the nudix domain is a C-terminal area called Box B, which helps bind Dcp2 to RNA.^[5] With all three of these main motifs, Dcp2 is able to find, bind firmly to, and hydrolyzes a 5' mRNA cap. It does this either by recognizing a hairpin loop in the RNA within 10 base pairs of the cap, which is called a Dcp2 binding and decapping element, or by a separate protein recognizing a base pair pattern in the mRNA and directly recruiting the Dcp2-Dcp1 holoenzyme.^[8] Unfortunately, Dcp2 works slowly, and needs a few other proteins to coordinate with it so it can decap mRNA in a timely manner.

Dcp1

Upf1, Upf2, and Upf3 are proteins involved in the regulatory pathway of nonsense-mediated mRNA decay, and not the actual decapping of mRNA. Only Upf1 attaches directly to the decapping complex, whereas Upf2 and Upf3 attach to mRNA, then attach to Upf1 to facilitate the destruction of incorrect mRNA. These are activators of the complex, in that they can direct the complex at incorrectly formed mRNA, but do not actually help decap the mRNA.^[8]

DDX6

P-bodies are essentially stockpiled clumps of decapped or repressed mRNA mixed together with mRNA degradation factors, such as the decapping complex and the nonsense-mediated mRNA decay machinery, so they are important for the eventual destruction of the mRNA altered by Dcp2.^[16] As Edc3 creates P-bodies around the decapping complex, it becomes easier for Dcp2 to find mRNA 5' caps to hydrolyze, increasing the effectiveness of the entire complex.^[17]

Pat1

Pat1 is another protein that increases the efficiency of the decapping complex.^[17] It has three main domains. One is necessary for decapping mRNA, and directly helps the Dcp2-Dcp1 holoenzyme do so. The other two make it easier for the protein to decap mRNA, but are not directly involved in the hydrolysis of the phosphate bond.^[16] Pat1 has many interactions with the various proteins in the decapping complex, and is known as the 'scaffolding protein' because it brings everything together when it is time to decap something. The N-terminus domain interacts with DXX6 and brings it close so it can activate Dcp1, another portion helps create P-bodies along with Edc3, and the C-terminus domains attach Dcp1–Dcp2, the Lsm1–7 complex and Xrn1 to the complex.^[5][18]

Xrn1