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| - | [[Image:2z41.jpg|left|200px]] | |
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| + | ==Crystal Structure Analysis of the Ski2-type RNA helicase== |
| - | The line below this paragraph, containing "STRUCTURE_2z41", creates the "Structure Box" on the page.
| + | <StructureSection load='2z41' size='340' side='right'caption='[[2z41]], [[Resolution|resolution]] 3.51Å' 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'>[[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> |
| - | 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]] 3.51Å</td></tr> |
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| + | <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> |
| - | {{STRUCTURE_2z41| PDB=2z41 | SCENE= }}
| + | <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> |
| - | '''Crystal Structure Analysis of the Ski2-type RNA helicase'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | 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.
| + | [[Category: Kakuta Y]] |
| - | | + | [[Category: Kimura M]] |
| - | ==About this Structure== | + | [[Category: Nakashima T]] |
| - | 2Z41 is a [[Single protein]] structure of sequence from [http://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].
| + | [[Category: Tanaka I]] |
| - | | + | [[Category: Yao M]] |
| - | ==Reference== | + | [[Category: Zhang X]] |
| - | 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:[http://www.ncbi.nlm.nih.gov/pubmed/18042682 18042682]
| + | |
| - | [[Category: Pyrococcus horikoshii]] | + | |
| - | [[Category: Single protein]] | + | |
| - | [[Category: Kakuta, Y.]] | + | |
| - | [[Category: Kimura, M.]] | + | |
| - | [[Category: Nakashima, T.]] | + | |
| - | [[Category: Tanaka, I.]] | + | |
| - | [[Category: Yao, M.]] | + | |
| - | [[Category: Zhang, X.]] | + | |
| - | [[Category: Dna helicase]]
| + | |
| - | [[Category: Hydrolase]]
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| - | [[Category: Rna helicase]]
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