1v2x: Difference between revisions

Latest revision as of 23:56, 27 December 2023

TrmH

Structural highlights

1v2x is a 1 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	PO4, SAM
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

TRMH_THET8 Catalyzes the 2'-O methylation of guanosine at position 18 in tRNA. Type I methylase, which methylates all tRNAs.^[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

The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 A resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2'-OH group for methylation.

Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme.,Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, Yokoyama S Structure. 2004 Apr;12(4):593-602. PMID:15062082^[5]

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

References

↑ Hori H, Suzuki T, Sugawara K, Inoue Y, Shibata T, Kuramitsu S, Yokoyama S, Oshima T, Watanabe K. Identification and characterization of tRNA (Gm18) methyltransferase from Thermus thermophilus HB8: domain structure and conserved amino acid sequence motifs. Genes Cells. 2002 Mar;7(3):259-72. PMID:11918670 doi:10.1046/j.1365-2443.2002.00520.x
↑ Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, Yokoyama S. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure. 2004 Apr;12(4):593-602. PMID:15062082 doi:10.1016/j.str.2004.03.003
↑ Ochi A, Makabe K, Kuwajima K, Hori H. Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes. J Biol Chem. 2010 Mar 19;285(12):9018-29. PMID:20053984 doi:10.1074/jbc.M109.065698
↑ Ochi A, Makabe K, Yamagami R, Hirata A, Sakaguchi R, Hou YM, Watanabe K, Nureki O, Kuwajima K, Hori H. The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process. J Biol Chem. 2013 Aug 30;288(35):25562-25574. PMID:23867454 doi:10.1074/jbc.M113.485128
↑ Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, Yokoyama S. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure. 2004 Apr;12(4):593-602. PMID:15062082 doi:10.1016/j.str.2004.03.003

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Hori H, Suzuki T, Sugawara K, Inoue Y, Shibata T, Kuramitsu S, Yokoyama S, Oshima T, Watanabe K. Identification and characterization of tRNA (Gm18) methyltransferase from Thermus thermophilus HB8: domain structure and conserved amino acid sequence motifs. Genes Cells. 2002 Mar;7(3):259-72. PMID:11918670 doi:10.1046/j.1365-2443.2002.00520.x

[2] Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, Yokoyama S. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure. 2004 Apr;12(4):593-602. PMID:15062082 doi:10.1016/j.str.2004.03.003

[3] Ochi A, Makabe K, Kuwajima K, Hori H. Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes. J Biol Chem. 2010 Mar 19;285(12):9018-29. PMID:20053984 doi:10.1074/jbc.M109.065698

[4] Ochi A, Makabe K, Yamagami R, Hirata A, Sakaguchi R, Hou YM, Watanabe K, Nureki O, Kuwajima K, Hori H. The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process. J Biol Chem. 2013 Aug 30;288(35):25562-25574. PMID:23867454 doi:10.1074/jbc.M113.485128

[5] Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, Yokoyama S. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure. 2004 Apr;12(4):593-602. PMID:15062082 doi:10.1016/j.str.2004.03.003

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[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
 ==TrmH==
-<StructureSection load='1v2x' size='340' side='right' caption='[[1v2x]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<StructureSection load='1v2x' size='340' side='right'caption='[[1v2x]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1v2x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V2X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1v2x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V2X FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanosine(18)-2'-O)-methyltransferase tRNA (guanosine(18)-2'-O)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.34 2.1.1.34] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></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=1v2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v2x OCA], [http://pdbe.org/1v2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v2x RCSB], [http://www.ebi.ac.uk/pdbsum/1v2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v2x ProSAT], [http://www.topsan.org/Proteins/RSGI/1v2x TOPSAN]</span></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=1v2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v2x OCA], [https://pdbe.org/1v2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v2x RCSB], [https://www.ebi.ac.uk/pdbsum/1v2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v2x ProSAT], [https://www.topsan.org/Proteins/RSGI/1v2x TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRMH_THET8 TRMH_THET8] Catalyzes the 2'-O methylation of guanosine at position 18 in tRNA. Type I methylase, which methylates all tRNAs.<ref>PMID:11918670</ref> <ref>PMID:15062082</ref> <ref>PMID:20053984</ref> <ref>PMID:23867454</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
+[[Category: Large Structures]]
-[[Category: Endo, Y]]
+[[Category: Thermus thermophilus]]
-[[Category: Fukai, S]]
+[[Category: Endo Y]]
-[[Category: Hori, H]]
+[[Category: Fukai S]]
-[[Category: Ishii, R]]
+[[Category: Hori H]]
-[[Category: Nureki, O]]
+[[Category: Ishii R]]
-[[Category: Structural genomic]]
+[[Category: Nureki O]]
-[[Category: Watanabe, K]]
+[[Category: Watanabe K]]
-[[Category: Yokoyama, S]]
+[[Category: Yokoyama S]]
-[[Category: Deep trefoil knot]]
-[[Category: Rsgi]]
-[[Category: Transferase]]

1v2x: Difference between revisions

Latest revision as of 23:56, 27 December 2023

TrmH

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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