1x1p: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 3: / Line 3: @@
 <StructureSection load='1x1p' size='340' side='right'caption='[[1x1p]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1x1p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X1P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1x1p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X1P FirstGlance]. <br>
-</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></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]] 2.8&#8491;</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=1x1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1p OCA], [https://pdbe.org/1x1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x1p RCSB], [https://www.ebi.ac.uk/pdbsum/1x1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x1p ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RNH2_THEKO RNH2_THEKO]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
+[https://www.uniprot.org/uniprot/RNH2_THEKO RNH2_THEKO] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 19: / Line 19: @@
 </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=1x1p ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Conformational studies on amyloid beta peptide (Abeta) in aqueous solution are complicated by its tendency to aggregate. In this study, we determined the atomic-level structure of Abeta(28-42) in an aqueous environment. We fused fragments of Abeta, residues 10-24 (Abeta(10-24)) or 28-42 (Abeta(28-42)), to three positions in the C-terminal region of ribonuclease HII from a hyperthermophile, Thermococcus kodakaraensis (Tk-RNase HII). We then examined the structural properties in an aqueous environment. The host protein, Tk-RNase HII, is highly stable and the C-terminal region has relatively little interaction with other parts. CD spectroscopy and thermal denaturation experiments demonstrated that the guest amyloidogenic sequences did not affect the overall structure of the Tk-RNase HII. Crystal structure analysis of Tk-RNase HII(1-197)-Abeta(28-42) revealed that Abeta(28-42) forms a beta conformation, whereas the original structure in Tk-RNase HII(1-213) was alpha helix, suggesting beta-structure formation of Abeta(28-42) within full-length Abeta in aqueous solution. Abeta(28-42) enhanced aggregation of the host protein more strongly than Abeta(10-24). These results and other reports suggest that after proteolytic cleavage, the C-terminal region of Abeta adopts a beta conformation in an aqueous environment and induces aggregation, and that the central region of Abeta plays a critical role in fibril formation. This study also indicates that this fusion technique is useful for obtaining structural information with atomic resolution for amyloidogenic peptides in aqueous environments.
-Structure of amyloid beta fragments in aqueous environments.,Takano K, Endo S, Mukaiyama A, Chon H, Matsumura H, Koga Y, Kanaya S FEBS J. 2006 Jan;273(1):150-8. PMID:16367755<ref>PMID:16367755</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1x1p" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Ribonuclease H]]
+[[Category: Thermococcus kodakarensis KOD1]]
-[[Category: Chon, H]]
+[[Category: Chon H]]
-[[Category: Endo, S]]
+[[Category: Endo S]]
-[[Category: Kanaya, S]]
+[[Category: Kanaya S]]
-[[Category: Koga, Y]]
+[[Category: Koga Y]]
-[[Category: Matsumura, H]]
+[[Category: Matsumura H]]
-[[Category: Mukaiyama, A]]
+[[Category: Mukaiyama A]]
-[[Category: Takano, K]]
+[[Category: Takano K]]
-[[Category: Amyloid peptide]]
-[[Category: Hydrolase]]
-[[Category: Ribonuclease hii]]
-[[Category: Thermococcus kodakaraensis]]