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| | <StructureSection load='1vdx' size='340' side='right'caption='[[1vdx]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='1vdx' size='340' side='right'caption='[[1vdx]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1vdx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VDX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1vdx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VDX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=1vdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vdx OCA], [http://pdbe.org/1vdx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vdx RCSB], [http://www.ebi.ac.uk/pdbsum/1vdx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vdx ProSAT], [http://www.topsan.org/Proteins/RSGI/1vdx TOPSAN]</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=1vdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vdx OCA], [https://pdbe.org/1vdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vdx RCSB], [https://www.ebi.ac.uk/pdbsum/1vdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vdx ProSAT], [https://www.topsan.org/Proteins/RSGI/1vdx TOPSAN]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/THPR_PYRHO THPR_PYRHO] Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.[HAMAP-Rule:MF_01940] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrococcus shinkaii]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Structural genomic]] | + | [[Category: Pyrococcus horikoshii]] |
| - | [[Category: Rehse, P H]] | + | [[Category: Rehse PH]] |
| - | [[Category: Tahirov, T H]] | + | [[Category: Tahirov TH]] |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| Structural highlights
Function
THPR_PYRHO 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
Cyclic phosphodiesterase and 2'-5' RNA ligase are members of a superfamily of proteins which share structural similarities even though their homology may be very low. A putative 2'-5' RNA ligase from Pyrococcus horikoshii has been crystallized and its X-ray crystallographic structure determined to 2.4 A. The protein crystallized in the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 44.07, b = 45.47, c = 93.17 A and one protein monomer in the asymmetric unit. The molecular-replacement probe was a 2'-5' RNA ligase from Thermus thermophilus which shares 30% sequence identity. The P. horikoshii RNA ligase has some structural features that have more in common with a cyclic phosphodiesterase from Arabidopsis thaliana with which it has no significant homology, yet an examination of the electrostatic surface potential clearly defines its relationship to the T. thermophilus RNA ligase. However, the size of the active-site cleft is smaller and less positively charged than that of the T. thermophilus homologue, suggesting that the actual substrate may be smaller than that previously postulated for the latter.
Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii.,Rehse PH, Tahirov TH Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1207-12. Epub 2005, Aug 16. PMID:16131753[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Rehse PH, Tahirov TH. Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii. Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1207-12. Epub 2005, Aug 16. PMID:16131753 doi:10.1107/S0907444905017841
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