|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA== | | ==tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA== |
| - | <StructureSection load='3b0v' size='340' side='right' caption='[[3b0v]], [[Resolution|resolution]] 3.51Å' scene=''> | + | <StructureSection load='3b0v' size='340' side='right'caption='[[3b0v]], [[Resolution|resolution]] 3.51Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3b0v]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B0V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B0V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3b0v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B0V FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene><br> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.51Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3b0p|3b0p]], [[3b0u|3b0u]]</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=3b0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b0v OCA], [https://pdbe.org/3b0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b0v RCSB], [https://www.ebi.ac.uk/pdbsum/3b0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b0v ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA0016 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
| + | </table> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3b0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b0v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b0v RCSB], [http://www.ebi.ac.uk/pdbsum/3b0v PDBsum]</span></td></tr>
| + | == Function == |
| - | <table> | + | [https://www.uniprot.org/uniprot/DUSAL_THET8 DUSAL_THET8] Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U20 and U20a in tRNAs.[HAMAP-Rule:MF_02041]<ref>PMID:22123979</ref> <ref>PMID:25902496</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 15: |
Line 16: |
| | Molecular basis of dihydrouridine formation on tRNA.,Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):19593-8. Epub 2011 Nov 28. PMID:22123979<ref>PMID:22123979</ref> | | Molecular basis of dihydrouridine formation on tRNA.,Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):19593-8. Epub 2011 Nov 28. PMID:22123979<ref>PMID:22123979</ref> |
| | | | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3b0v" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Thermus thermophilus]] | + | [[Category: Large Structures]] |
| - | [[Category: Nakamura, A.]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Tanaka, I.]] | + | [[Category: Nakamura A]] |
| - | [[Category: Tanaka, Y.]] | + | [[Category: Tanaka I]] |
| - | [[Category: Yamashita, K.]] | + | [[Category: Tanaka Y]] |
| - | [[Category: Yao, M.]] | + | [[Category: Yamashita K]] |
| - | [[Category: Yu, F.]] | + | [[Category: Yao M]] |
| - | [[Category: Oxidoreductase-rna complex]]
| + | [[Category: Yu F]] |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
DUSAL_THET8 Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U20 and U20a in tRNAs.[HAMAP-Rule:MF_02041][1] [2]
Publication Abstract from PubMed
Dihydrouridine (D) is a highly conserved modified base found in tRNAs from all domains of life. Dihydrouridine synthase (Dus) catalyzes the D formation of tRNA through reduction of uracil base with flavin mononucleotide (FMN) as a cofactor. Here, we report the crystal structures of Thermus thermophilus Dus (TthDus), which is responsible for D formation at positions 20 and 20a, in complex with tRNA and with a short fragment of tRNA (D-loop). Dus interacts extensively with the D-arm and recognizes the elbow region composed of the kissing loop interaction between T- and D-loops in tRNA, pulling U20 into the catalytic center for reduction. Although distortion of the D-loop structure was observed upon binding of Dus to tRNA, the canonical D-loop/T-loop interaction was maintained. These results were consistent with the observation that Dus preferentially recognizes modified rather than unmodified tRNAs, indicating that Dus introduces D20 by monitoring the complete L-shaped structure of tRNAs. In the active site, U20 is stacked on the isoalloxazine ring of FMN, and C5 of the U20 uracil ring is covalently cross linked to the thiol group of Cys93, implying a catalytic mechanism of D20 formation. In addition, the involvement of a cofactor molecule in uracil ring recognition was proposed. Based on a series of mutation analyses, we propose a molecular basis of tRNA recognition and D formation catalyzed by Dus.
Molecular basis of dihydrouridine formation on tRNA.,Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):19593-8. Epub 2011 Nov 28. PMID:22123979[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I. Molecular basis of dihydrouridine formation on tRNA. Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):19593-8. Epub 2011 Nov 28. PMID:22123979 doi:10.1073/pnas.1112352108
- ↑ Byrne RT, Jenkins HT, Peters DT, Whelan F, Stowell J, Aziz N, Kasatsky P, Rodnina MV, Koonin EV, Konevega AL, Antson AA. Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases. Proc Natl Acad Sci U S A. 2015 Apr 22. pii: 201500161. PMID:25902496 doi:http://dx.doi.org/10.1073/pnas.1500161112
- ↑ Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I. Molecular basis of dihydrouridine formation on tRNA. Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):19593-8. Epub 2011 Nov 28. PMID:22123979 doi:10.1073/pnas.1112352108
|
