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| | ==Crystal Structure of APE0204 from Aeropyrum pernix== | | ==Crystal Structure of APE0204 from Aeropyrum pernix== |
| - | <StructureSection load='1wfx' size='340' side='right' caption='[[1wfx]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='1wfx' size='340' side='right'caption='[[1wfx]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1wfx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WFX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1wfx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WFX 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.8Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APE0204 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 AERPX])</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=1wfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wfx OCA], [https://pdbe.org/1wfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wfx RCSB], [https://www.ebi.ac.uk/pdbsum/1wfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wfx ProSAT], [https://www.topsan.org/Proteins/RSGI/1wfx TOPSAN]</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=1wfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wfx OCA], [http://pdbe.org/1wfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wfx RCSB], [http://www.ebi.ac.uk/pdbsum/1wfx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wfx ProSAT], [http://www.topsan.org/Proteins/RSGI/1wfx TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KPTA_AERPE KPTA_AERPE]] Removes the 2'-phosphate from RNA via an intermediate in which the phosphate is ADP-ribosylated by NAD followed by a presumed transesterification to release the RNA and generate ADP-ribose 1''-2''-cyclic phosphate (APPR>P). May function as an ADP-ribosylase (By similarity). | + | [https://www.uniprot.org/uniprot/KPTA_AERPE KPTA_AERPE] Removes the 2'-phosphate from RNA via an intermediate in which the phosphate is ADP-ribosylated by NAD followed by a presumed transesterification to release the RNA and generate ADP-ribose 1''-2''-cyclic phosphate (APPR>P). May function as an ADP-ribosylase (By similarity). |
| | == 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: Aerpx]] | + | [[Category: Aeropyrum pernix]] |
| - | [[Category: Bessho, Y]] | + | [[Category: Large Structures]] |
| - | [[Category: Kato-Murayama, M]] | + | [[Category: Bessho Y]] |
| - | [[Category: Structural genomic]] | + | [[Category: Kato-Murayama M]] |
| - | [[Category: Shirouzu, M]] | + | [[Category: Shirouzu M]] |
| - | [[Category: Yokoyama, S]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Nad]]
| + | |
| - | [[Category: Rna 2'-phosphotransferase]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Trna splicing]]
| + | |
| Structural highlights
Function
KPTA_AERPE Removes the 2'-phosphate from RNA via an intermediate in which the phosphate is ADP-ribosylated by NAD followed by a presumed transesterification to release the RNA and generate ADP-ribose 1-2-cyclic phosphate (APPR>P). May function as an ADP-ribosylase (By similarity).
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
In the final step of tRNA splicing, the 2'-phosphotransferase catalyzes the transfer of the extra 2'-phosphate from the precursor-ligated tRNA to NAD. We have determined the crystal structure of the 2'-phosphotransferase protein from Aeropyrum pernix K1 at 2.8 Angstroms resolution. The structure of the 2'-phosphotransferase contains two globular domains (N and C-domains), which form a cleft in the center. The N-domain has the winged helix motif, a subfamily of the helix-turn-helix family, which is shared by many DNA-binding proteins. The C-domain of the 2'-phosphotransferase superimposes well on the NAD-binding fold of bacterial (diphtheria) toxins, which catalyze the transfer of ADP ribose from NAD to target proteins, indicating that the mode of NAD binding by the 2'-phosphotransferase could be similar to that of the bacterial toxins. The conserved basic residues are assembled at the periphery of the cleft and could participate in the enzyme contact with the sugar-phosphate backbones of tRNA. The modes by which the two functional domains recognize the two different substrates are clarified by the present crystal structure of the 2'-phosphotransferase.
Crystal structure of the RNA 2'-phosphotransferase from Aeropyrum pernix K1.,Kato-Murayama M, Bessho Y, Shirouzu M, Yokoyama S J Mol Biol. 2005 Apr 29;348(2):295-305. PMID:15811369[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kato-Murayama M, Bessho Y, Shirouzu M, Yokoyama S. Crystal structure of the RNA 2'-phosphotransferase from Aeropyrum pernix K1. J Mol Biol. 2005 Apr 29;348(2):295-305. PMID:15811369 doi:10.1016/j.jmb.2005.02.049
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