This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3htx

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 20:20, 5 August 2016

Crystal structure of small RNA methyltransferase HEN1

Structural highlights

3htx is a 6 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	HEN1 (ARATH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[HEN1_ARATH] Methyltransferase that adds a methyl group to the ribose of the last nucleotide of small RNAs (sRNAs). This protects the 3'-end of sRNAs from uridylation activity and subsequent degradation. Can methylate 3'-end of microRNAs (miRNAs), small interfering RNAs (siRNas) and trans-acting small interfering RNAs (ta-siRNAs). Involved in plant development through its role in small RNAs processing. Required for the specification of reproductive organ identities and the probable repression of A class genes. May control floral determinacy possibly by regulating the expression of the C class floral homeotic gene AGAMOUS (AG).^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

RNA silencing is a conserved regulatory mechanism in fungi, plants and animals that regulates gene expression and defence against viruses and transgenes. Small silencing RNAs of approximately 20-30 nucleotides and their associated effector proteins, the Argonaute family proteins, are the central components in RNA silencing. A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2'-O-methylation on the 3' terminal nucleotide. A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification. Here we report the 3.1 A crystal structure of full-length HEN1 from Arabidopsis in complex with a 22-nucleotide small RNA duplex and cofactor product S-adenosyl-l-homocysteine. Highly cooperative recognition of the small RNA substrate by multiple RNA binding domains and the methyltransferase domain in HEN1 measures the length of the RNA duplex and determines the substrate specificity. Metal ion coordination by both 2' and 3' hydroxyls on the 3'-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel Mg(2+)-dependent 2'-O-methylation mechanism.

Structural insights into mechanisms of the small RNA methyltransferase HEN1.,Huang Y, Ji L, Huang Q, Vassylyev DG, Chen X, Ma JB Nature. 2009 Oct 8;461(7265):823-7. PMID:19812675^[5]

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

References

↑ Chen X, Liu J, Cheng Y, Jia D. HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development. 2002 Mar;129(5):1085-94. PMID:11874905
↑ Suzuki M, Takahashi T, Komeda Y. Formation of corymb-like inflorescences due to delay in bolting and flower development in the corymbosa2 mutant of Arabidopsis. Plant Cell Physiol. 2002 Mar;43(3):298-306. PMID:11917084
↑ Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X. Methylation as a crucial step in plant microRNA biogenesis. Science. 2005 Feb 11;307(5711):932-5. PMID:15705854 doi:http://dx.doi.org/10.1126/science.1107130
↑ Li J, Yang Z, Yu B, Liu J, Chen X. Methylation protects miRNAs and siRNAs from a 3'-end uridylation activity in Arabidopsis. Curr Biol. 2005 Aug 23;15(16):1501-7. PMID:16111943 doi:http://dx.doi.org/10.1016/j.cub.2005.07.029
↑ Huang Y, Ji L, Huang Q, Vassylyev DG, Chen X, Ma JB. Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature. 2009 Oct 8;461(7265):823-7. PMID:19812675 doi:10.1038/nature08433

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3htx"

@@ Line 1: / Line 1: @@
 ==Crystal structure of small RNA methyltransferase HEN1==
 <StructureSection load='3htx' size='340' side='right' caption='[[3htx]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3htx]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HTX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HTX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3htx]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HTX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HTX FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HEN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HEN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3htx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3htx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3htx RCSB], [http://www.ebi.ac.uk/pdbsum/3htx PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3htx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3htx OCA], [http://pdbe.org/3htx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3htx RCSB], [http://www.ebi.ac.uk/pdbsum/3htx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3htx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q945R3_ARATH Q945R3_ARATH]] Methyltransferase that adds a methyl group to the ribose of the last nucleotide of small RNAs (sRNAs). This protects the 3'-end of sRNAs from uridylation activity and subsequent degradation. Can methylate 3'-end of microRNAs (miRNAs), small interfering RNAs (siRNas) and trans-acting small interfering RNAs (ta-siRNAs). Involved in plant development through its role in small RNAs processing. Required for the specification of reproductive organ identities and the probable repression of A class genes. May control floral determinacy possibly by regulating the expression of the C class floral homeotic gene AGAMOUS (AG).<ref>PMID:11874905</ref> <ref>PMID:11917084</ref> <ref>PMID:15705854</ref> <ref>PMID:16111943</ref>
+[[http://www.uniprot.org/uniprot/HEN1_ARATH HEN1_ARATH]] Methyltransferase that adds a methyl group to the ribose of the last nucleotide of small RNAs (sRNAs). This protects the 3'-end of sRNAs from uridylation activity and subsequent degradation. Can methylate 3'-end of microRNAs (miRNAs), small interfering RNAs (siRNas) and trans-acting small interfering RNAs (ta-siRNAs). Involved in plant development through its role in small RNAs processing. Required for the specification of reproductive organ identities and the probable repression of A class genes. May control floral determinacy possibly by regulating the expression of the C class floral homeotic gene AGAMOUS (AG).<ref>PMID:11874905</ref> <ref>PMID:11917084</ref> <ref>PMID:15705854</ref> <ref>PMID:16111943</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 18: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3htx ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3htx" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arabidopsis thaliana]]
+[[Category: Arath]]
 [[Category: Chen, X M]]
 [[Category: Huang, Q C]]

3htx

From Proteopedia

Revision as of 20:20, 5 August 2016

Crystal structure of small RNA methyltransferase HEN1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox