5e8j: Difference between revisions

Latest revision as of 06:17, 5 July 2023

Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with RAM

Structural highlights

5e8j is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.35Å
Ligands:	GOL, SAH
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MCES_HUMAN mRNA-capping methyltransferase that methylates the N7 position of the added guanosine to the 5'-cap structure of mRNAs. Binds RNA containing 5'-terminal GpppC.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Maturation and translation of mRNA in eukaryotes requires the addition of the 7-methylguanosine cap. In vertebrates, the cap methyltransferase, RNA guanine-7 methyltransferase (RNMT), has an activating subunit, RNMT-Activating Miniprotein (RAM). Here we report the first crystal structure of the human RNMT in complex with the activation domain of RAM. A relatively unstructured and negatively charged RAM binds to a positively charged surface groove on RNMT, distal to the active site. This results in stabilisation of a RNMT lobe structure which co-evolved with RAM and is required for RAM binding. Structure-guided mutagenesis and molecular dynamics simulations reveal that RAM stabilises the structure and positioning of the RNMT lobe and the adjacent alpha-helix hinge, resulting in optimal positioning of helix A which contacts substrates in the active site. Using biophysical and biochemical approaches, we observe that RAM increases the recruitment of the methyl donor, AdoMet (S-adenosyl methionine), to RNMT. Thus we report the mechanism by which RAM allosterically activates RNMT, allowing it to function as a molecular rheostat for mRNA cap methylation.

Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM.,Varshney D, Petit AP, Bueren-Calabuig JA, Jansen C, Fletcher DA, Peggie M, Weidlich S, Scullion P, Pisliakov AV, Cowling VH Nucleic Acids Res. 2016 Jul 15. pii: gkw637. PMID:27422871^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tsukamoto T, Shibagaki Y, Niikura Y, Mizumoto K. Cloning and characterization of three human cDNAs encoding mRNA (guanine-7-)-methyltransferase, an mRNA cap methylase. Biochem Biophys Res Commun. 1998 Oct 9;251(1):27-34. PMID:9790902 doi:https://dx.doi.org/S0006-291X(98)99402-5
↑ Pillutla RC, Yue Z, Maldonado E, Shatkin AJ. Recombinant human mRNA cap methyltransferase binds capping enzyme/RNA polymerase IIo complexes. J Biol Chem. 1998 Aug 21;273(34):21443-6. PMID:9705270
↑ Saha N, Schwer B, Shuman S. Characterization of human, Schizosaccharomyces pombe, and Candida albicans mRNA cap methyltransferases and complete replacement of the yeast capping apparatus by mammalian enzymes. J Biol Chem. 1999 Jun 4;274(23):16553-62. PMID:10347220
↑ Gonatopoulos-Pournatzis T, Dunn S, Bounds R, Cowling VH. RAM/Fam103a1 is required for mRNA cap methylation. Mol Cell. 2011 Nov 18;44(4):585-96. doi: 10.1016/j.molcel.2011.08.041. PMID:22099306 doi:https://dx.doi.org/10.1016/j.molcel.2011.08.041
↑ Varshney D, Petit AP, Bueren-Calabuig JA, Jansen C, Fletcher DA, Peggie M, Weidlich S, Scullion P, Pisliakov AV, Cowling VH. Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Nucleic Acids Res. 2016 Jul 15. pii: gkw637. PMID:27422871 doi:https://dx.doi.org/10.1093/nar/gkw637

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Tsukamoto T, Shibagaki Y, Niikura Y, Mizumoto K. Cloning and characterization of three human cDNAs encoding mRNA (guanine-7-)-methyltransferase, an mRNA cap methylase. Biochem Biophys Res Commun. 1998 Oct 9;251(1):27-34. PMID:9790902 doi:https://dx.doi.org/S0006-291X(98)99402-5

[2] Pillutla RC, Yue Z, Maldonado E, Shatkin AJ. Recombinant human mRNA cap methyltransferase binds capping enzyme/RNA polymerase IIo complexes. J Biol Chem. 1998 Aug 21;273(34):21443-6. PMID:9705270

[3] Saha N, Schwer B, Shuman S. Characterization of human, Schizosaccharomyces pombe, and Candida albicans mRNA cap methyltransferases and complete replacement of the yeast capping apparatus by mammalian enzymes. J Biol Chem. 1999 Jun 4;274(23):16553-62. PMID:10347220

[4] Gonatopoulos-Pournatzis T, Dunn S, Bounds R, Cowling VH. RAM/Fam103a1 is required for mRNA cap methylation. Mol Cell. 2011 Nov 18;44(4):585-96. doi: 10.1016/j.molcel.2011.08.041. PMID:22099306 doi:https://dx.doi.org/10.1016/j.molcel.2011.08.041

[5] Varshney D, Petit AP, Bueren-Calabuig JA, Jansen C, Fletcher DA, Peggie M, Weidlich S, Scullion P, Pisliakov AV, Cowling VH. Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Nucleic Acids Res. 2016 Jul 15. pii: gkw637. PMID:27422871 doi:https://dx.doi.org/10.1093/nar/gkw637

[1]

[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5e8j is ON HOLD
+==Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with RAM==
+<StructureSection load='5e8j' size='340' side='right'caption='[[5e8j]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5e8j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E8J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E8J FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5e8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e8j OCA], [https://pdbe.org/5e8j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e8j RCSB], [https://www.ebi.ac.uk/pdbsum/5e8j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e8j ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MCES_HUMAN MCES_HUMAN] mRNA-capping methyltransferase that methylates the N7 position of the added guanosine to the 5'-cap structure of mRNAs. Binds RNA containing 5'-terminal GpppC.<ref>PMID:9790902</ref> <ref>PMID:9705270</ref> <ref>PMID:10347220</ref> <ref>PMID:22099306</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Maturation and translation of mRNA in eukaryotes requires the addition of the 7-methylguanosine cap. In vertebrates, the cap methyltransferase, RNA guanine-7 methyltransferase (RNMT), has an activating subunit, RNMT-Activating Miniprotein (RAM). Here we report the first crystal structure of the human RNMT in complex with the activation domain of RAM. A relatively unstructured and negatively charged RAM binds to a positively charged surface groove on RNMT, distal to the active site. This results in stabilisation of a RNMT lobe structure which co-evolved with RAM and is required for RAM binding. Structure-guided mutagenesis and molecular dynamics simulations reveal that RAM stabilises the structure and positioning of the RNMT lobe and the adjacent alpha-helix hinge, resulting in optimal positioning of helix A which contacts substrates in the active site. Using biophysical and biochemical approaches, we observe that RAM increases the recruitment of the methyl donor, AdoMet (S-adenosyl methionine), to RNMT. Thus we report the mechanism by which RAM allosterically activates RNMT, allowing it to function as a molecular rheostat for mRNA cap methylation.
-Authors: Petit, P., Cowling, V.
+Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM.,Varshney D, Petit AP, Bueren-Calabuig JA, Jansen C, Fletcher DA, Peggie M, Weidlich S, Scullion P, Pisliakov AV, Cowling VH Nucleic Acids Res. 2016 Jul 15. pii: gkw637. PMID:27422871<ref>PMID:27422871</ref>
-Description: Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with RAM
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Petit, P]]
+<div class="pdbe-citations 5e8j" style="background-color:#fffaf0;"></div>
-[[Category: Cowling, V]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Cowling V]]
+[[Category: Petit P]]

5e8j: Difference between revisions

Latest revision as of 06:17, 5 July 2023

Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with RAM

Structural highlights

Function

Publication Abstract from PubMed

References

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