1udx: Difference between revisions

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-[[Image:1udx.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1udx", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_1udx|  PDB=1udx  |  SCENE=  }}
-'''Crystal structure of the conserved protein TT1381 from Thermus thermophilus HB8'''
+==Crystal structure of the conserved protein TT1381 from Thermus thermophilus HB8==
+<StructureSection load='1udx' size='340' side='right'caption='[[1udx]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1udx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDX FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.07&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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=1udx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udx OCA], [https://pdbe.org/1udx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udx RCSB], [https://www.ebi.ac.uk/pdbsum/1udx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udx ProSAT], [https://www.topsan.org/Proteins/RSGI/1udx TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OBG_THET8 OBG_THET8] An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate (By similarity). It may play a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control (Potential).[HAMAP-Rule:MF_01454]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ud/1udx_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1udx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Obg comprises a unique family of high-molecular mass GTPases conserved from bacteria to eukaryotes. Bacterial Obg is essential for cellular growth, sporulation, and differentiation. Here, we report the crystal structure of the full-length form of Obg from Thermus thermophilus HB8 at 2.07 A resolution, in the nucleotide-free state. It reveals a three-domain arrangement, composed of the N-terminal domain, the guanine nucleotide-binding domain (G domain), and the C-terminal domain. The N-terminal and G domains have the Obg fold and the Ras-like fold, respectively. These global folds are similar to those of the recently published structure of the C-terminal domain-truncated form of Obg from Bacillus subtilis. On the other hand, the C-terminal domain of Obg was found to have a novel fold (the OCT fold). A comparison of the T.thermophilus and B.subtilis nucleotide-free Obg structures revealed significant conformational changes in the switch-I and switch-II regions of the G domain. Notably, the N-terminal domain is rotated drastically, by almost 180 degrees, around the G domain axis. In the T.thermophilus Obg crystal, the nucleotide-binding site of the G domain interacts with the C-terminal domain of the adjacent molecule. These data suggest a possible domain rearrangement of Obg, and a potential role of the C-terminal domain in the regulation of the nucleotide-binding state.
-==Overview==
+Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8.,Kukimoto-Niino M, Murayama K, Inoue M, Terada T, Tame JR, Kuramitsu S, Shirouzu M, Yokoyama S J Mol Biol. 2004 Mar 26;337(3):761-70. PMID:15019792<ref>PMID:15019792</ref>
-Obg comprises a unique family of high-molecular mass GTPases conserved from bacteria to eukaryotes. Bacterial Obg is essential for cellular growth, sporulation, and differentiation. Here, we report the crystal structure of the full-length form of Obg from Thermus thermophilus HB8 at 2.07 A resolution, in the nucleotide-free state. It reveals a three-domain arrangement, composed of the N-terminal domain, the guanine nucleotide-binding domain (G domain), and the C-terminal domain. The N-terminal and G domains have the Obg fold and the Ras-like fold, respectively. These global folds are similar to those of the recently published structure of the C-terminal domain-truncated form of Obg from Bacillus subtilis. On the other hand, the C-terminal domain of Obg was found to have a novel fold (the OCT fold). A comparison of the T.thermophilus and B.subtilis nucleotide-free Obg structures revealed significant conformational changes in the switch-I and switch-II regions of the G domain. Notably, the N-terminal domain is rotated drastically, by almost 180 degrees, around the G domain axis. In the T.thermophilus Obg crystal, the nucleotide-binding site of the G domain interacts with the C-terminal domain of the adjacent molecule. These data suggest a possible domain rearrangement of Obg, and a potential role of the C-terminal domain in the regulation of the nucleotide-binding state.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-UDX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UDX OCA].
+</div>
+<div class="pdbe-citations 1udx" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8., Kukimoto-Niino M, Murayama K, Inoue M, Terada T, Tame JR, Kuramitsu S, Shirouzu M, Yokoyama S, J Mol Biol. 2004 Mar 26;337(3):761-70. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15019792 15019792]
+*[[GTP-binding protein 3D structures|GTP-binding protein 3D structures]]
-[[Category: Single protein]]
+== References ==
-[[Category: Thermus thermophilus]]
+<references/>
-[[Category: Inoue, M.]]
+__TOC__
-[[Category: Kukimoto-Niino, M.]]
+</StructureSection>
-[[Category: Kuramitsu, S.]]
+[[Category: Large Structures]]
-[[Category: Murayama, K.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Inoue M]]
-[[Category: Shirouzu, M.]]
+[[Category: Kukimoto-Niino M]]
-[[Category: Yokoyama, S.]]
+[[Category: Kuramitsu S]]
-[[Category: Gtp-binding protein]]
+[[Category: Murayama K]]
-[[Category: Obg]]
+[[Category: Shirouzu M]]
-[[Category: Riken structural genomics/proteomics initiative]]
+[[Category: Yokoyama S]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-[[Category: Tgs domain]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 11:05:00 2008''