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==Pyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cognate tRNA== | ==Pyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cognate tRNA== | ||
<StructureSection load='5wt1' size='340' side='right' caption='[[5wt1]], [[Resolution|resolution]] 2.60Å' scene=''> | <StructureSection load='5wt1' size='340' side='right'caption='[[5wt1]], [[Resolution|resolution]] 2.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5wt1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WT1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WT1 FirstGlance]. <br> | <table><tr><td colspan='2'>[[5wt1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrab Pyrab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WT1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WT1 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wt3|5wt3]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wt3|5wt3]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">trm5a, PYRAB01130, PAB2272 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</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='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=5wt1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wt1 OCA], [http://pdbe.org/5wt1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wt1 RCSB], [http://www.ebi.ac.uk/pdbsum/5wt1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wt1 ProSAT]</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=5wt1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wt1 OCA], [http://pdbe.org/5wt1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wt1 RCSB], [http://www.ebi.ac.uk/pdbsum/5wt1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wt1 ProSAT]</span></td></tr> | ||
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== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/TRM5A_PYRAB TRM5A_PYRAB]] Specifically methylates the N1 position of guanosine-37 in tRNA(Phe). In vitro, can also methylate the C7 position of 4-demethylwyosine (imG-14).<ref>PMID:20382657</ref> | [[http://www.uniprot.org/uniprot/TRM5A_PYRAB TRM5A_PYRAB]] Specifically methylates the N1 position of guanosine-37 in tRNA(Phe). In vitro, can also methylate the C7 position of 4-demethylwyosine (imG-14).<ref>PMID:20382657</ref> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The wyosine derivatives present at position 37 in transfer RNAs (tRNAs) are critical for reading frame maintenance. The methyltransferase Trm5a from Pyrococcus abyssi (PaTrm5a) plays a key role in this hypermodification process in generating m(1)G37 and imG2, two products of the wyosine biosynthetic pathway, through two methyl transfers to distinct substrates, but the mechanism is currently unknown. We report two cocrystal structures of PaTrm5a in complex with tRNA(Phe) and reveal the structural basis for substrate recognition, which was supported by in vitro activity assays. The crystal structures showed that the D1 domain of the enzyme undergoes large conformational changes upon the binding of tRNA. The deletion of this domain greatly reduces the affinity and activity of PaTrm5a toward its RNA substrate, indicating that the enzyme recognizes the overall shape of tRNA. Using the small-angle x-ray scattering technique and crystallographic analysis, we discovered that PaTrm5a adopts distinct open conformations before and after the binding of tRNA. Last, through structure comparison with its ortholog Methanococcus jannaschii Trm5b (MjTrm5b), we propose a reaction mechanism for the double methylation capability of this unique enzyme. | |||
Structural insight into the methyltransfer mechanism of the bifunctional Trm5.,Wang C, Jia Q, Zeng J, Chen R, Xie W Sci Adv. 2017 Dec 1;3(12):e1700195. doi: 10.1126/sciadv.1700195. eCollection 2017, Dec. PMID:29214216<ref>PMID:29214216</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5wt1" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Pyrab]] | |||
[[Category: Jia, Q]] | [[Category: Jia, Q]] | ||
[[Category: Wang, C]] | [[Category: Wang, C]] | ||
Revision as of 12:12, 18 December 2019
Pyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cognate tRNAPyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cognate tRNA
Structural highlights
Function[TRM5A_PYRAB] Specifically methylates the N1 position of guanosine-37 in tRNA(Phe). In vitro, can also methylate the C7 position of 4-demethylwyosine (imG-14).[1] Publication Abstract from PubMedThe wyosine derivatives present at position 37 in transfer RNAs (tRNAs) are critical for reading frame maintenance. The methyltransferase Trm5a from Pyrococcus abyssi (PaTrm5a) plays a key role in this hypermodification process in generating m(1)G37 and imG2, two products of the wyosine biosynthetic pathway, through two methyl transfers to distinct substrates, but the mechanism is currently unknown. We report two cocrystal structures of PaTrm5a in complex with tRNA(Phe) and reveal the structural basis for substrate recognition, which was supported by in vitro activity assays. The crystal structures showed that the D1 domain of the enzyme undergoes large conformational changes upon the binding of tRNA. The deletion of this domain greatly reduces the affinity and activity of PaTrm5a toward its RNA substrate, indicating that the enzyme recognizes the overall shape of tRNA. Using the small-angle x-ray scattering technique and crystallographic analysis, we discovered that PaTrm5a adopts distinct open conformations before and after the binding of tRNA. Last, through structure comparison with its ortholog Methanococcus jannaschii Trm5b (MjTrm5b), we propose a reaction mechanism for the double methylation capability of this unique enzyme. Structural insight into the methyltransfer mechanism of the bifunctional Trm5.,Wang C, Jia Q, Zeng J, Chen R, Xie W Sci Adv. 2017 Dec 1;3(12):e1700195. doi: 10.1126/sciadv.1700195. eCollection 2017, Dec. PMID:29214216[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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