6jp6

From Proteopedia

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Revision as of 07:19, 16 October 2019

The X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential for 2'-O-methylation at the first position of anticodon in specific tRNAs

Structural highlights

6jp6 is a 4 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Activity:	tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase, with EC number 2.1.1.205
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[WDR6_YEAST] Involved in regulation of Ty1 transposition. Plays also a role in the regulation of the retromer complex and is required for the recycling from endosomes of plasma membrane proteins like CAN1 and MUP1. Required together with TRM7 for the methylation of the 2'-O-ribose of nucleotides at position 34 of the tRNA anticodon loop of tRNA(Phe) and tRNA(Leu(UAA)).^[1] ^[2] ^[3] [TRM7_YEAST] Methylates the 2'-O-ribose of nucleotides at positions 32 and 34 of the tRNA anticodon loop of tRNA(Phe), tRNA(Trp) and tRNA(Leu(UAA)). Requires TRM732 for methylation of the cytidine at position 32 and RTT10/TRM734 for methylation of the nucleotides at position 34 in substrate tRNAs. Lack of either of these modifications in tRNA(Phe) reduces formation of wybutosine from 1-methylguanosine at position 37.^[4] ^[5]

Publication Abstract from PubMed

The complex between Trm7 and Trm734 (Trm7-Trm734) from Saccharomyces cerevisiae catalyzes 2'-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7-Trm734 complex. Purified recombinant Trm7-Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7-Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7-Trm734. Small angle X-ray scattering reveals that Trm7-Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 beta-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7-Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.

Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.,Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H Nucleic Acids Res. 2019 Oct 5. pii: 5581736. doi: 10.1093/nar/gkz856. PMID:31586407^[6]

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

References

↑ Nyswaner KM, Checkley MA, Yi M, Stephens RM, Garfinkel DJ. Chromatin-associated genes protect the yeast genome from Ty1 insertional mutagenesis. Genetics. 2008 Jan;178(1):197-214. doi: 10.1534/genetics.107.082602. PMID:18202368 doi:http://dx.doi.org/10.1534/genetics.107.082602
↑ Shi Y, Stefan CJ, Rue SM, Teis D, Emr SD. Two novel WD40 domain-containing proteins, Ere1 and Ere2, function in the retromer-mediated endosomal recycling pathway. Mol Biol Cell. 2011 Nov;22(21):4093-107. doi: 10.1091/mbc.E11-05-0440. Epub 2011 , Aug 31. PMID:21880895 doi:http://dx.doi.org/10.1091/mbc.E11-05-0440
↑ Guy MP, Podyma BM, Preston MA, Shaheen HH, Krivos KL, Limbach PA, Hopper AK, Phizicky EM. Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. RNA. 2012 Oct;18(10):1921-33. doi: 10.1261/rna.035287.112. Epub 2012 Aug 21. PMID:22912484 doi:http://dx.doi.org/10.1261/rna.035287.112
↑ Pintard L, Lecointe F, Bujnicki JM, Bonnerot C, Grosjean H, Lapeyre B. Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop. EMBO J. 2002 Apr 2;21(7):1811-20. doi: 10.1093/emboj/21.7.1811. PMID:11927565 doi:http://dx.doi.org/10.1093/emboj/21.7.1811
↑ Guy MP, Podyma BM, Preston MA, Shaheen HH, Krivos KL, Limbach PA, Hopper AK, Phizicky EM. Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. RNA. 2012 Oct;18(10):1921-33. doi: 10.1261/rna.035287.112. Epub 2012 Aug 21. PMID:22912484 doi:http://dx.doi.org/10.1261/rna.035287.112
↑ Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H. Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition. Nucleic Acids Res. 2019 Oct 5. pii: 5581736. doi: 10.1093/nar/gkz856. PMID:31586407 doi:http://dx.doi.org/10.1093/nar/gkz856

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6jp6"

@@ Line 3: / Line 3: @@
 <StructureSection load='6jp6' size='340' side='right'caption='[[6jp6]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6jp6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JP6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JP6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6jp6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JP6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JP6 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(cytidine(32)/guanosine(34)-2'-O)-methyltransferase tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.205 2.1.1.205] </span></td></tr>
@@ Line 10: / Line 10: @@
 == Function ==
 [[http://www.uniprot.org/uniprot/WDR6_YEAST WDR6_YEAST]] Involved in regulation of Ty1 transposition. Plays also a role in the regulation of the retromer complex and is required for the recycling from endosomes of plasma membrane proteins like CAN1 and MUP1. Required together with TRM7 for the methylation of the 2'-O-ribose of nucleotides at position 34 of the tRNA anticodon loop of tRNA(Phe) and tRNA(Leu(UAA)).<ref>PMID:18202368</ref> <ref>PMID:21880895</ref> <ref>PMID:22912484</ref>  [[http://www.uniprot.org/uniprot/TRM7_YEAST TRM7_YEAST]] Methylates the 2'-O-ribose of nucleotides at positions 32 and 34 of the tRNA anticodon loop of tRNA(Phe), tRNA(Trp) and tRNA(Leu(UAA)). Requires TRM732 for methylation of the cytidine at position 32 and RTT10/TRM734 for methylation of the nucleotides at position 34 in substrate tRNAs. Lack of either of these modifications in tRNA(Phe) reduces formation of wybutosine from 1-methylguanosine at position 37.<ref>PMID:11927565</ref> <ref>PMID:22912484</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The complex between Trm7 and Trm734 (Trm7-Trm734) from Saccharomyces cerevisiae catalyzes 2'-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7-Trm734 complex. Purified recombinant Trm7-Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7-Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7-Trm734. Small angle X-ray scattering reveals that Trm7-Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 beta-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7-Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.
+Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.,Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H Nucleic Acids Res. 2019 Oct 5. pii: 5581736. doi: 10.1093/nar/gkz856. PMID:31586407<ref>PMID:31586407</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6jp6" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Baker's yeast]]
 [[Category: Large Structures]]
 [[Category: Hirata, A]]

6jp6

From Proteopedia

Revision as of 07:19, 16 October 2019

The X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential for 2'-O-methylation at the first position of anticodon in specific tRNAs

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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