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| | <StructureSection load='2z41' size='340' side='right'caption='[[2z41]], [[Resolution|resolution]] 3.51Å' scene=''> | | <StructureSection load='2z41' size='340' side='right'caption='[[2z41]], [[Resolution|resolution]] 3.51Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2z41]] 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=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z41 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2z41]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z41 FirstGlance]. <br> |
| - | </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></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]] 3.51Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></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></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH1280 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [https://pdbe.org/2z41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [https://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [https://pdbe.org/2z41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [https://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 ProSAT]</span></td></tr> |
| | </table> | | </table> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyrococcus horikoshii]] | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | [[Category: Kakuta, Y]] | + | [[Category: Kakuta Y]] |
| - | [[Category: Kimura, M]] | + | [[Category: Kimura M]] |
| - | [[Category: Nakashima, T]] | + | [[Category: Nakashima T]] |
| - | [[Category: Tanaka, I]] | + | [[Category: Tanaka I]] |
| - | [[Category: Yao, M]] | + | [[Category: Yao M]] |
| - | [[Category: Zhang, X]] | + | [[Category: Zhang X]] |
| - | [[Category: Dna helicase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Rna helicase]]
| + | |
| Structural highlights
Publication Abstract from PubMed
The Ski complex composed of Ski2p, Ski3p, and Ski8p plays an essential role in the 3' to 5' cytoplasmic mRNA degradation pathway in yeast. Ski2p is a putative RNA helicase, belonging in the DExD/H-box protein families and conserved in eukarya as well as in archaea. The gene product (Ph1280p) from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 shows sequence homology with Ski2p, sharing 22.6% identical amino acids with a central region of Ski2p. In order to gain structural information about the Ski2p-like RNA helicase, we overproduced Ph1280p in Escherichia coli cells, and purified it to apparent homogeneity. Ph1280p exhibits DNA/RNA-dependent ATPase activity with an optimal temperature at approximately 90 degrees C. The crystal structure of Ph1280p has been solved at a resolution of 3.5 A using single-wavelength anomalous dispersion (SAD) and selenomethionyl (Se-Met)-substituted protein. Ph1280p comprises four subdomains; the two N-terminal subdomains (N1 and N2) fold into an RecA-like architecture with the conserved helicase motifs, while the two C-terminal subdomains (C1 and C2) fold into alpha-helical structures containing a winged helix (WH)-fold and helix-hairpin-helix (HhH)-fold, respectively. Although the structure of each of the Ph1280p subdomains can be individually superimposed on the corresponding domains in other helicases, such as the Escherichia coli DNA helicase RecQ, the relative orientation of the helicase and C-terminal subdomains in Ph1280p is significantly different from that of other helicases. This structural feature is implicated in substrate specificity for the Ski2-like helicase and would play a critical role in the 3' to 5' cytoplasmic mRNA degradation in the Ski complex.
Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.,Zhang X, Nakashima T, Kakuta Y, Yao M, Tanaka I, Kimura M Protein Sci. 2008 Jan;17(1):136-45. Epub 2007 Nov 27. PMID:18042682[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Zhang X, Nakashima T, Kakuta Y, Yao M, Tanaka I, Kimura M. Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3. Protein Sci. 2008 Jan;17(1):136-45. Epub 2007 Nov 27. PMID:18042682 doi:ps.073107008
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