9z3d: Difference between revisions

Revision as of 07:04, 3 June 2026

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to a pre-tRNA Leu(CAA) intron

Structural highlights

9z3d is a 2 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:	Electron Microscopy, Resolution 2.96Å
Ligands:	A1CZ2, SAH
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

NSUN2_HUMAN Autosomal recessive non-syndromic intellectual disability;Dubowitz syndrome. The disease is caused by variants affecting the gene represented in this entry.

Function

NSUN2_HUMAN RNA cytosine C(5)-methyltransferase that methylates cytosine to 5-methylcytosine (m5C) in various RNAs, such as tRNAs, mRNAs and some long non-coding RNAs (lncRNAs) (PubMed:17071714, PubMed:22995836, PubMed:31199786, PubMed:31358969). Involved in various processes, such as epidermal stem cell differentiation, testis differentiation and maternal to zygotic transition during early development: acts by increasing protein synthesis; cytosine C(5)-methylation promoting tRNA stability and preventing mRNA decay (PubMed:31199786). Methylates cytosine to 5-methylcytosine (m5C) at positions 34 and 48 of intron-containing tRNA(Leu)(CAA) precursors, and at positions 48, 49 and 50 of tRNA(Gly)(GCC) precursors (PubMed:17071714, PubMed:22995836, PubMed:31199786). tRNA methylation is required generation of RNA fragments derived from tRNAs (tRFs) (PubMed:31199786). Also mediates C(5)-methylation of mitochondrial tRNAs (PubMed:31276587). Catalyzes cytosine C(5)-methylation of mRNAs, leading to stabilize them and prevent mRNA decay: mRNA stabilization involves YBX1 that specifically recognizes and binds m5C-modified transcripts (PubMed:22395603, PubMed:31358969, PubMed:34556860). Cytosine C(5)-methylation of mRNAs also regulates mRNA export: methylated transcripts are specifically recognized by THOC4/ALYREF, which mediates mRNA nucleo-cytoplasmic shuttling (PubMed:28418038). Also mediates cytosine C(5)-methylation of non-coding RNAs, such as vault RNAs (vtRNAs), promoting their processing into regulatory small RNAs (PubMed:23871666). Cytosine C(5)-methylation of vtRNA VTRNA1.1 promotes its processing into small-vault RNA4 (svRNA4) and regulates epidermal differentiation (PubMed:31186410). May act downstream of Myc to regulate epidermal cell growth and proliferation (By similarity). Required for proper spindle assembly and chromosome segregation, independently of its methyltransferase activity (PubMed:19596847).[UniProtKB:Q1HFZ0]^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

References

↑ Brzezicha B, Schmidt M, Makalowska I, Jarmolowski A, Pienkowska J, Szweykowska-Kulinska Z. Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA Leu (CAA). Nucleic Acids Res. 2006;34(20):6034-43. PMID:17071714 doi:10.1093/nar/gkl765
↑ Hussain S, Benavente SB, Nascimento E, Dragoni I, Kurowski A, Gillich A, Humphreys P, Frye M. The nucleolar RNA methyltransferase Misu (NSun2) is required for mitotic spindle stability. J Cell Biol. 2009 Jul 13;186(1):27-40. PMID:19596847 doi:10.1083/jcb.200810180
↑ Zhang X, Liu Z, Yi J, Tang H, Xing J, Yu M, Tong T, Shang Y, Gorospe M, Wang W. The tRNA methyltransferase NSun2 stabilizes p16INK⁴ mRNA by methylating the 3'-untranslated region of p16. Nat Commun. 2012 Mar 6;3:712. PMID:22395603 doi:10.1038/ncomms1692
↑ Auxilien S, Guérineau V, Szweykowska-Kulińska Z, Golinelli-Pimpaneau B. The human tRNA m (5) C methyltransferase Misu is multisite-specific. RNA Biol. 2012 Nov;9(11):1331-8. PMID:22995836 doi:10.4161/rna.22180
↑ Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, Paramor M, Gleeson JG, Odom DT, Ule J, Frye M. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep. 2013 Jul 25;4(2):255-61. PMID:23871666 doi:10.1016/j.celrep.2013.06.029
↑ Yang X, Yang Y, Sun BF, Chen YS, Xu JW, Lai WY, Li A, Wang X, Bhattarai DP, Xiao W, Sun HY, Zhu Q, Ma HL, Adhikari S, Sun M, Hao YJ, Zhang B, Huang CM, Huang N, Jiang GB, Zhao YL, Wang HL, Sun YP, Yang YG. 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m(5)C reader. Cell Res. 2017 May;27(5):606-625. doi: 10.1038/cr.2017.55. Epub 2017 Apr 18. PMID:28418038 doi:https://dx.doi.org/10.1038/cr.2017.55
↑ Sajini AA, Choudhury NR, Wagner RE, Bornelov S, Selmi T, Spanos C, Dietmann S, Rappsilber J, Michlewski G, Frye M. Loss of 5-methylcytosine alters the biogenesis of vault-derived small RNAs to coordinate epidermal differentiation. Nat Commun. 2019 Jun 11;10(1):2550. doi: 10.1038/s41467-019-10020-7. PMID:31186410 doi:https://dx.doi.org/10.1038/s41467-019-10020-7
↑ Gkatza NA, Castro C, Harvey RF, Heiss M, Popis MC, Blanco S, Bornelov S, Sajini AA, Gleeson JG, Griffin JL, West JA, Kellner S, Willis AE, Dietmann S, Frye M. Cytosine-5 RNA methylation links protein synthesis to cell metabolism. PLoS Biol. 2019 Jun 14;17(6):e3000297. doi: 10.1371/journal.pbio.3000297. , eCollection 2019 Jun. PMID:31199786 doi:https://dx.doi.org/10.1371/journal.pbio.3000297
↑ Van Haute L, Lee SY, McCann BJ, Powell CA, Bansal D, Vasiliauskaite L, Garone C, Shin S, Kim JS, Frye M, Gleeson JG, Miska EA, Rhee HW, Minczuk M. NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs. Nucleic Acids Res. 2019 Sep 19;47(16):8720-8733. doi: 10.1093/nar/gkz559. PMID:31276587 doi:https://dx.doi.org/10.1093/nar/gkz559
↑ Chen X, Li A, Sun BF, Yang Y, Han YN, Yuan X, Chen RX, Wei WS, Liu Y, Gao CC, Chen YS, Zhang M, Ma XD, Liu ZW, Luo JH, Lyu C, Wang HL, Ma J, Zhao YL, Zhou FJ, Huang Y, Xie D, Yang YG. 5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs. Nature cell biology. 2019 Aug 1. doi: 10.1038/s41556-019-0361-y. PMID: 31358969.
↑ Dai W, Li A, Yu NJ, Nguyen T, Leach RW, Wuhr M, Kleiner RE. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Nat Chem Biol. 2021 Nov;17(11):1178-1187. doi: 10.1038/s41589-021-00874-8. Epub , 2021 Sep 23. PMID:34556860 doi:https://dx.doi.org/10.1038/s41589-021-00874-8

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Brzezicha B, Schmidt M, Makalowska I, Jarmolowski A, Pienkowska J, Szweykowska-Kulinska Z. Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA Leu (CAA). Nucleic Acids Res. 2006;34(20):6034-43. PMID:17071714 doi:10.1093/nar/gkl765

[2] Hussain S, Benavente SB, Nascimento E, Dragoni I, Kurowski A, Gillich A, Humphreys P, Frye M. The nucleolar RNA methyltransferase Misu (NSun2) is required for mitotic spindle stability. J Cell Biol. 2009 Jul 13;186(1):27-40. PMID:19596847 doi:10.1083/jcb.200810180

[3] Zhang X, Liu Z, Yi J, Tang H, Xing J, Yu M, Tong T, Shang Y, Gorospe M, Wang W. The tRNA methyltransferase NSun2 stabilizes p16INK⁴ mRNA by methylating the 3'-untranslated region of p16. Nat Commun. 2012 Mar 6;3:712. PMID:22395603 doi:10.1038/ncomms1692

[4] Auxilien S, Guérineau V, Szweykowska-Kulińska Z, Golinelli-Pimpaneau B. The human tRNA m (5) C methyltransferase Misu is multisite-specific. RNA Biol. 2012 Nov;9(11):1331-8. PMID:22995836 doi:10.4161/rna.22180

[5] Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, Paramor M, Gleeson JG, Odom DT, Ule J, Frye M. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep. 2013 Jul 25;4(2):255-61. PMID:23871666 doi:10.1016/j.celrep.2013.06.029

[6] Yang X, Yang Y, Sun BF, Chen YS, Xu JW, Lai WY, Li A, Wang X, Bhattarai DP, Xiao W, Sun HY, Zhu Q, Ma HL, Adhikari S, Sun M, Hao YJ, Zhang B, Huang CM, Huang N, Jiang GB, Zhao YL, Wang HL, Sun YP, Yang YG. 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m(5)C reader. Cell Res. 2017 May;27(5):606-625. doi: 10.1038/cr.2017.55. Epub 2017 Apr 18. PMID:28418038 doi:https://dx.doi.org/10.1038/cr.2017.55

[7] Sajini AA, Choudhury NR, Wagner RE, Bornelov S, Selmi T, Spanos C, Dietmann S, Rappsilber J, Michlewski G, Frye M. Loss of 5-methylcytosine alters the biogenesis of vault-derived small RNAs to coordinate epidermal differentiation. Nat Commun. 2019 Jun 11;10(1):2550. doi: 10.1038/s41467-019-10020-7. PMID:31186410 doi:https://dx.doi.org/10.1038/s41467-019-10020-7

[8] Gkatza NA, Castro C, Harvey RF, Heiss M, Popis MC, Blanco S, Bornelov S, Sajini AA, Gleeson JG, Griffin JL, West JA, Kellner S, Willis AE, Dietmann S, Frye M. Cytosine-5 RNA methylation links protein synthesis to cell metabolism. PLoS Biol. 2019 Jun 14;17(6):e3000297. doi: 10.1371/journal.pbio.3000297. , eCollection 2019 Jun. PMID:31199786 doi:https://dx.doi.org/10.1371/journal.pbio.3000297

[9] Van Haute L, Lee SY, McCann BJ, Powell CA, Bansal D, Vasiliauskaite L, Garone C, Shin S, Kim JS, Frye M, Gleeson JG, Miska EA, Rhee HW, Minczuk M. NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs. Nucleic Acids Res. 2019 Sep 19;47(16):8720-8733. doi: 10.1093/nar/gkz559. PMID:31276587 doi:https://dx.doi.org/10.1093/nar/gkz559

[10] Chen X, Li A, Sun BF, Yang Y, Han YN, Yuan X, Chen RX, Wei WS, Liu Y, Gao CC, Chen YS, Zhang M, Ma XD, Liu ZW, Luo JH, Lyu C, Wang HL, Ma J, Zhao YL, Zhou FJ, Huang Y, Xie D, Yang YG. 5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs. Nature cell biology. 2019 Aug 1. doi: 10.1038/s41556-019-0361-y. PMID: 31358969.

[11] Dai W, Li A, Yu NJ, Nguyen T, Leach RW, Wuhr M, Kleiner RE. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Nat Chem Biol. 2021 Nov;17(11):1178-1187. doi: 10.1038/s41589-021-00874-8. Epub , 2021 Sep 23. PMID:34556860 doi:https://dx.doi.org/10.1038/s41589-021-00874-8

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9z3d is ON HOLD  until Paper Publication
+==CryoEM structure of human NSUN2(C271A) with SAH cross-linked to a pre-tRNA Leu(CAA) intron==
+<StructureSection load='9z3d' size='340' side='right'caption='[[9z3d]], [[Resolution|resolution]] 2.96&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9z3d]] is a 2 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=9Z3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9Z3D FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.96&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1CZ2:[(2~{R},3~{S},4~{R},5~{R})-5-[(5~{R})-6-azanyl-5-methyl-2-oxidanylidene-4,5-dihydropyrimidin-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>A1CZ2</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=9z3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9z3d OCA], [https://pdbe.org/9z3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9z3d RCSB], [https://www.ebi.ac.uk/pdbsum/9z3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9z3d ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/NSUN2_HUMAN NSUN2_HUMAN] Autosomal recessive non-syndromic intellectual disability;Dubowitz syndrome. The disease is caused by variants affecting the gene represented in this entry.
+== Function ==
+[https://www.uniprot.org/uniprot/NSUN2_HUMAN NSUN2_HUMAN] RNA cytosine C(5)-methyltransferase that methylates cytosine to 5-methylcytosine (m5C) in various RNAs, such as tRNAs, mRNAs and some long non-coding RNAs (lncRNAs) (PubMed:17071714, PubMed:22995836, PubMed:31199786, PubMed:31358969). Involved in various processes, such as epidermal stem cell differentiation, testis differentiation and maternal to zygotic transition during early development: acts by increasing protein synthesis; cytosine C(5)-methylation promoting tRNA stability and preventing mRNA decay (PubMed:31199786). Methylates cytosine to 5-methylcytosine (m5C) at positions 34 and 48 of intron-containing tRNA(Leu)(CAA) precursors, and at positions 48, 49 and 50 of tRNA(Gly)(GCC) precursors (PubMed:17071714, PubMed:22995836, PubMed:31199786). tRNA methylation is required generation of RNA fragments derived from tRNAs (tRFs) (PubMed:31199786). Also mediates C(5)-methylation of mitochondrial tRNAs (PubMed:31276587). Catalyzes cytosine C(5)-methylation of mRNAs, leading to stabilize them and prevent mRNA decay: mRNA stabilization involves YBX1 that specifically recognizes and binds m5C-modified transcripts (PubMed:22395603, PubMed:31358969, PubMed:34556860). Cytosine C(5)-methylation of mRNAs also regulates mRNA export: methylated transcripts are specifically recognized by THOC4/ALYREF, which mediates mRNA nucleo-cytoplasmic shuttling (PubMed:28418038). Also mediates cytosine C(5)-methylation of non-coding RNAs, such as vault RNAs (vtRNAs), promoting their processing into regulatory small RNAs (PubMed:23871666). Cytosine C(5)-methylation of vtRNA VTRNA1.1 promotes its processing into small-vault RNA4 (svRNA4) and regulates epidermal differentiation (PubMed:31186410). May act downstream of Myc to regulate epidermal cell growth and proliferation (By similarity). Required for proper spindle assembly and chromosome segregation, independently of its methyltransferase activity (PubMed:19596847).[UniProtKB:Q1HFZ0]<ref>PMID:17071714</ref> <ref>PMID:19596847</ref> <ref>PMID:22395603</ref> <ref>PMID:22995836</ref> <ref>PMID:23871666</ref> <ref>PMID:28418038</ref> <ref>PMID:31186410</ref> <ref>PMID:31199786</ref> <ref>PMID:31276587</ref> <ref>PMID:31358969</ref> <ref>PMID:34556860</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Canepa J]]
+[[Category: Nam Y]]
+[[Category: Ruiz-Arroyo VM]]

9z3d: Difference between revisions

Revision as of 07:04, 3 June 2026

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to a pre-tRNA Leu(CAA) intron

Structural highlights

Disease

Function

References

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