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4yvi

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Revision as of 07:28, 10 May 2023

Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA

Structural highlights

4yvi is a 3 chain structure with sequence from Haemophilus influenzae Rd KW20 and Thermotoga maritima MSB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TRMD_HAEIN Specifically methylates guanosine-37 in various tRNAs (By similarity).[HAMAP-Rule:MF_00605]

Publication Abstract from PubMed

The deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life. In bacteria, TrmD catalyzes the N(1)-methylguanosine (m(1)G) modification at position 37 in transfer RNAs (tRNAs) with the (36)GG(37) sequence, using S-adenosyl-l-methionine (AdoMet) as the methyl donor. The m(1)G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome. Here we report the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. Our structural analysis revealed the mechanism by which TrmD binds the substrate tRNA in an AdoMet-dependent manner. The trefoil-knot center, which is structurally conserved among SPOUT MTases, accommodates the adenosine moiety of AdoMet by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of AdoMet, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m(1)G37-tRNA.

Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.,Ito T, Masuda I, Yoshida K, Goto-Ito S, Sekine S, Suh SW, Hou YM, Yokoyama S Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4197-205. doi:, 10.1073/pnas.1422981112. Epub 2015 Jul 16. PMID:26183229^[1]

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

References

↑ Ito T, Masuda I, Yoshida K, Goto-Ito S, Sekine S, Suh SW, Hou YM, Yokoyama S. Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD. Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4197-205. doi:, 10.1073/pnas.1422981112. Epub 2015 Jul 16. PMID:26183229 doi:http://dx.doi.org/10.1073/pnas.1422981112

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4yvi"

@@ Line 3: / Line 3: @@
 <StructureSection load='4yvi' size='340' side='right'caption='[[4yvi]], [[Resolution|resolution]] 3.01&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4yvi]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Haein Haein]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YVI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4yvi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_Rd_KW20 Haemophilus influenzae Rd KW20] and [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YVI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yvg|4yvg]], [[4yvh|4yvh]], [[4yvj|4yvj]], [[4yvk|4yvk]]</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=4yvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yvi OCA], [https://pdbe.org/4yvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yvi RCSB], [https://www.ebi.ac.uk/pdbsum/4yvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yvi ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">trmD, HI_0202 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </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=4yvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yvi OCA], [http://pdbe.org/4yvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yvi RCSB], [http://www.ebi.ac.uk/pdbsum/4yvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yvi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TRMD_HAEIN TRMD_HAEIN]] Specifically methylates guanosine-37 in various tRNAs (By similarity).[HAMAP-Rule:MF_00605]
+[https://www.uniprot.org/uniprot/TRMD_HAEIN TRMD_HAEIN] Specifically methylates guanosine-37 in various tRNAs (By similarity).[HAMAP-Rule:MF_00605]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 20: @@
 ==See Also==
-*[[TRNA methyltransferase|TRNA methyltransferase]]
+*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
 *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 == References ==
@@ Line 29: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Haein]]
+[[Category: Haemophilus influenzae Rd KW20]]
 [[Category: Large Structures]]
-[[Category: Ito, T]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Yokoyama, S]]
+[[Category: Ito T]]
-[[Category: Yoshida, K]]
+[[Category: Yokoyama S]]
-[[Category: Mtase]]
+[[Category: Yoshida K]]
-[[Category: Spout]]
-[[Category: Transferase-rna complex]]
-[[Category: Trna]]

4yvi

From Proteopedia

Revision as of 07:28, 10 May 2023

Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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