3eph

From Proteopedia

(Difference between revisions)

Revision as of 09:12, 23 February 2022

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

Structural highlights

3eph is a 4 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	3epj, 3epk, 3epl
Gene:	MOD5, YOR274W (ATCC 18824)
Activity:	tRNA dimethylallyltransferase, with EC number 2.5.1.75
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[MOD5_YEAST] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).^[1] ^[2] ^[3]

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

Hypermodifications near the anticodon of tRNA are fundamental for the efficiency and fidelity of protein synthesis. Dimethylallyltransferase (DMATase) catalyzes transfer of a dimethylallyl moiety from dimethylallyl pyrophosphate to N6 of A37 in certain tRNAs. Here we present the crystal structures of Saccharomyces cerevisiae DMATase-tRNA(Cys) complex in four distinct forms, which provide snapshots of the RNA modification reaction catalyzed by DMATase. The structures reveal that the enzyme recognizes the tRNA substrate through indirect sequence readout. The targeted nucleotide A37 flips out from the anticodon loop of tRNA and flips into a channel in DMATase, where it meets its reaction partner di methylallyl pyrophosphate, which enters the channel from the opposite end. Structural changes accompanying the transfer reaction taking place in the crystal result in disengagement of DMATase-tRNA interaction near the reaction center. In addition, structural comparison of DMATase in the complex with unliganded bacterial DMATase provides a molecular basis of ordered substrate binding by DMATase.

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism.,Zhou C, Huang RH Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16142-7. Epub 2008 Oct 13. PMID:18852462^[4]

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

References

↑ Dihanich ME, Najarian D, Clark R, Gillman EC, Martin NC, Hopper AK. Isolation and characterization of MOD5, a gene required for isopentenylation of cytoplasmic and mitochondrial tRNAs of Saccharomyces cerevisiae. Mol Cell Biol. 1987 Jan;7(1):177-84. PMID:3031456
↑ Benko AL, Vaduva G, Martin NC, Hopper AK. Competition between a sterol biosynthetic enzyme and tRNA modification in addition to changes in the protein synthesis machinery causes altered nonsense suppression. Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):61-6. PMID:10618371
↑ Lamichhane TN, Blewett NH, Maraia RJ. Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases. RNA. 2011 Oct;17(10):1846-57. doi: 10.1261/rna.2628611. Epub 2011 Aug 26. PMID:21873461 doi:http://dx.doi.org/10.1261/rna.2628611
↑ Zhou C, Huang RH. Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism. Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16142-7. Epub 2008 Oct 13. PMID:18852462

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism==
-<StructureSection load='3eph' size='340' side='right' caption='[[3eph]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
+<StructureSection load='3eph' size='340' side='right'caption='[[3eph]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3eph]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EPH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3eph]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPH 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=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3epj|3epj]], [[3epk|3epk]], [[3epl|3epl]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3epj|3epj]], [[3epk|3epk]], [[3epl|3epl]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MOD5, YOR274W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MOD5, YOR274W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_dimethylallyltransferase tRNA dimethylallyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.75 2.5.1.75] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/tRNA_dimethylallyltransferase tRNA dimethylallyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.75 2.5.1.75] </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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [http://pdbe.org/3eph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [http://www.ebi.ac.uk/pdbsum/3eph PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3eph ProSAT]</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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [https://pdbe.org/3eph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [https://www.ebi.ac.uk/pdbsum/3eph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eph ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MOD5_YEAST MOD5_YEAST]] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).<ref>PMID:3031456</ref> <ref>PMID:10618371</ref> <ref>PMID:21873461</ref>
+[[https://www.uniprot.org/uniprot/MOD5_YEAST MOD5_YEAST]] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).<ref>PMID:3031456</ref> <ref>PMID:10618371</ref> <ref>PMID:21873461</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 39: / Line 39: @@
 </StructureSection>
 [[Category: Atcc 18824]]
+[[Category: Large Structures]]
 [[Category: TRNA dimethylallyltransferase]]
 [[Category: Huang, R H]]

3eph

From Proteopedia

Revision as of 09:12, 23 February 2022

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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Proteopedia Page Contributors and Editors (what is this?)

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