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| - | [[Image:1iuh.gif|left|200px]] | |
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| - | <!-- | + | ==Crystal structure of TT0787 of thermus thermophilus HB8== |
| - | The line below this paragraph, containing "STRUCTURE_1iuh", creates the "Structure Box" on the page.
| + | <StructureSection load='1iuh' size='340' side='right'caption='[[1iuh]], [[Resolution|resolution]] 2.50Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet) | + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1iuh]] 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=1IUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IUH FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</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=1iuh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iuh OCA], [https://pdbe.org/1iuh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iuh RCSB], [https://www.ebi.ac.uk/pdbsum/1iuh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iuh ProSAT], [https://www.topsan.org/Proteins/RSGI/1iuh TOPSAN]</span></td></tr> |
| - | {{STRUCTURE_1iuh| PDB=1iuh | SCENE= }}
| + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/THPR_THET8 THPR_THET8] Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.[HAMAP-Rule:MF_01940] |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iu/1iuh_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1iuh ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | The 2'-5' RNA ligase family members are bacterial and archaeal RNA ligases that ligate 5' and 3' half-tRNA molecules with 2',3'-cyclic phosphate and 5'-hydroxyl termini, respectively, to the product containing the 2'-5' phosphodiester linkage. Here, the crystal structure of the 2'-5' RNA ligase protein from an extreme thermophile, Thermus thermophilus HB8, was solved at 2.5A resolution. The structure of the 2'-5' RNA ligase superimposes well on that of the Arabidopsis thaliana cyclic phosphodiesterase (CPDase), which hydrolyzes ADP-ribose 1",2"-cyclic phosphate (a product of the tRNA splicing reaction) to the monoester ADP-ribose 1"-phosphate. Although the sequence identity between the two proteins is remarkably low (9.3%), the 2'-5' RNA ligase and CPDase structures have two HX(T/S)X motifs in their corresponding positions. The HX(T/S)X motifs play important roles in the CPDase activity, and are conserved in both the CPDases and 2'-5' RNA ligases. Therefore, the catalytic mechanism of the 2'-5' RNA ligase may be similar to that of the CPDase. On the other hand, the electrostatic potential of the cavity of the 2'-5' RNA ligase is positive, but that of the CPDase is negative. Furthermore, in the CPDase, two loops with low B-factors cover the cavity. In contrast, in the 2'-5' RNA ligase, the corresponding loops form an open conformation and are flexible. These characteristics may be due to the differences in the substrates, tRNA and ADP-ribose 1",2"-cyclic phosphate. |
| | | | |
| - | '''Crystal structure of TT0787 of thermus thermophilus HB8'''
| + | Crystal structure of the 2'-5' RNA ligase from Thermus thermophilus HB8.,Kato M, Shirouzu M, Terada T, Yamaguchi H, Murayama K, Sakai H, Kuramitsu S, Yokoyama S J Mol Biol. 2003 Jun 20;329(5):903-11. PMID:12798681<ref>PMID:12798681</ref> |
| | | | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 1iuh" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Overview== | + | ==See Also== |
| - | The 2'-5' RNA ligase family members are bacterial and archaeal RNA ligases that ligate 5' and 3' half-tRNA molecules with 2',3'-cyclic phosphate and 5'-hydroxyl termini, respectively, to the product containing the 2'-5' phosphodiester linkage. Here, the crystal structure of the 2'-5' RNA ligase protein from an extreme thermophile, Thermus thermophilus HB8, was solved at 2.5A resolution. The structure of the 2'-5' RNA ligase superimposes well on that of the Arabidopsis thaliana cyclic phosphodiesterase (CPDase), which hydrolyzes ADP-ribose 1",2"-cyclic phosphate (a product of the tRNA splicing reaction) to the monoester ADP-ribose 1"-phosphate. Although the sequence identity between the two proteins is remarkably low (9.3%), the 2'-5' RNA ligase and CPDase structures have two HX(T/S)X motifs in their corresponding positions. The HX(T/S)X motifs play important roles in the CPDase activity, and are conserved in both the CPDases and 2'-5' RNA ligases. Therefore, the catalytic mechanism of the 2'-5' RNA ligase may be similar to that of the CPDase. On the other hand, the electrostatic potential of the cavity of the 2'-5' RNA ligase is positive, but that of the CPDase is negative. Furthermore, in the CPDase, two loops with low B-factors cover the cavity. In contrast, in the 2'-5' RNA ligase, the corresponding loops form an open conformation and are flexible. These characteristics may be due to the differences in the substrates, tRNA and ADP-ribose 1",2"-cyclic phosphate.
| + | *[[RNA ligase|RNA ligase]] |
| - | | + | == References == |
| - | ==About this Structure==
| + | <references/> |
| - | 1IUH is a [[Single protein]] structure of 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=1IUH OCA].
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==Reference== | + | [[Category: Large Structures]] |
| - | Crystal structure of the 2'-5' RNA ligase from Thermus thermophilus HB8., Kato M, Shirouzu M, Terada T, Yamaguchi H, Murayama K, Sakai H, Kuramitsu S, Yokoyama S, J Mol Biol. 2003 Jun 20;329(5):903-11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12798681 12798681]
| + | |
| - | [[Category: Single protein]]
| + | |
| - | [[Category: Thermus thermophilus]]
| + | |
| - | [[Category: Kato, M.]]
| + | |
| - | [[Category: Kuramitsu, S.]]
| + | |
| - | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
| + | |
| - | [[Category: Sakai, H.]]
| + | |
| - | [[Category: Shirouzu, M.]]
| + | |
| - | [[Category: Yokoyama, S.]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Riken structural genomics/proteomics initiative]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Structural genomic]] | + | |
| | [[Category: Thermus thermophilus]] | | [[Category: Thermus thermophilus]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 20:25:57 2008''
| + | [[Category: Kato M]] |
| | + | [[Category: Kuramitsu S]] |
| | + | [[Category: Sakai H]] |
| | + | [[Category: Shirouzu M]] |
| | + | [[Category: Yokoyama S]] |
| Structural highlights
Function
THPR_THET8 Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.[HAMAP-Rule:MF_01940]
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 2'-5' RNA ligase family members are bacterial and archaeal RNA ligases that ligate 5' and 3' half-tRNA molecules with 2',3'-cyclic phosphate and 5'-hydroxyl termini, respectively, to the product containing the 2'-5' phosphodiester linkage. Here, the crystal structure of the 2'-5' RNA ligase protein from an extreme thermophile, Thermus thermophilus HB8, was solved at 2.5A resolution. The structure of the 2'-5' RNA ligase superimposes well on that of the Arabidopsis thaliana cyclic phosphodiesterase (CPDase), which hydrolyzes ADP-ribose 1",2"-cyclic phosphate (a product of the tRNA splicing reaction) to the monoester ADP-ribose 1"-phosphate. Although the sequence identity between the two proteins is remarkably low (9.3%), the 2'-5' RNA ligase and CPDase structures have two HX(T/S)X motifs in their corresponding positions. The HX(T/S)X motifs play important roles in the CPDase activity, and are conserved in both the CPDases and 2'-5' RNA ligases. Therefore, the catalytic mechanism of the 2'-5' RNA ligase may be similar to that of the CPDase. On the other hand, the electrostatic potential of the cavity of the 2'-5' RNA ligase is positive, but that of the CPDase is negative. Furthermore, in the CPDase, two loops with low B-factors cover the cavity. In contrast, in the 2'-5' RNA ligase, the corresponding loops form an open conformation and are flexible. These characteristics may be due to the differences in the substrates, tRNA and ADP-ribose 1",2"-cyclic phosphate.
Crystal structure of the 2'-5' RNA ligase from Thermus thermophilus HB8.,Kato M, Shirouzu M, Terada T, Yamaguchi H, Murayama K, Sakai H, Kuramitsu S, Yokoyama S J Mol Biol. 2003 Jun 20;329(5):903-11. PMID:12798681[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kato M, Shirouzu M, Terada T, Yamaguchi H, Murayama K, Sakai H, Kuramitsu S, Yokoyama S. Crystal structure of the 2'-5' RNA ligase from Thermus thermophilus HB8. J Mol Biol. 2003 Jun 20;329(5):903-11. PMID:12798681
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