1u0l

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:43, 14 February 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1u0l.jpg|left|200px]]<br /><applet load="1u0l" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1u0l, resolution 2.80&Aring;" />
 
-
'''Crystal structure of YjeQ from Thermotoga maritima'''<br />
 
-
==Overview==
+
==Crystal structure of YjeQ from Thermotoga maritima==
-
We have determined the crystal structure of the GDP complex of the YjeQ protein from Thermotoga maritima (TmYjeQ), a member of the YjeQ GTPase subfamaily. TmYjeQ, a homologue of Escherichia coli YjeQ, which is known to bind to the ribosome, is composed of three domains: an N-terminal oligonucleotide/oligosaccharide-binding fold domain, a central GTPase domain, and a C-terminal zinc-finger domain. The crystal structure of TmYjeQ reveals two interesting domains: a circularly permutated GTPase domain and an unusual zinc-finger domain. The binding mode of GDP in the GTPase domain of TmYjeQ is similar to those of GDP or GTP analogs in ras proteins, a prototype GTPase. The N-terminal oligonucleotide/oligosaccharide-binding fold domain, together with the GTPase domain, forms the extended RNA-binding site. The C-terminal domain has an unusual zinc-finger motif composed of Cys-250, Cys-255, Cys-263, and His-257, with a remote structural similarity to a portion of a DNA-repair protein, rad51 fragment. The overall structural features of TmYjeQ make it a good candidate for an RNA-binding protein, which is consistent with the biochemical data of the YjeQ subfamily in binding to the ribosome.
+
<StructureSection load='1u0l' size='340' side='right'caption='[[1u0l]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1u0l]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U0L FirstGlance]. <br>
-
1U0L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=GDP:'>GDP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0L OCA].
+
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1u0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0l OCA], [https://pdbe.org/1u0l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u0l RCSB], [https://www.ebi.ac.uk/pdbsum/1u0l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u0l ProSAT], [https://www.topsan.org/Proteins/BSGC/1u0l TOPSAN]</span></td></tr>
-
Crystal structure of YjeQ from Thermotoga maritima contains a circularly permuted GTPase domain., Shin DH, Lou Y, Jancarik J, Yokota H, Kim R, Kim SH, Proc Natl Acad Sci U S A. 2004 Sep 7;101(36):13198-203. Epub 2004 Aug 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15331784 15331784]
+
</table>
-
[[Category: Single protein]]
+
== Function ==
 +
[https://www.uniprot.org/uniprot/RSGA_THEMA RSGA_THEMA] May play a role in 30S ribosomal subunit biogenesis. Unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover.[HAMAP-Rule:MF_01820]
 +
== 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/u0/1u0l_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=1u0l ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
-
[[Category: BSGC, Berkeley Structural Genomics Center.]]
+
[[Category: Jaru J]]
-
[[Category: Jaru, J.]]
+
[[Category: Kim R]]
-
[[Category: Kim, R.]]
+
[[Category: Kim SH]]
-
[[Category: Kim, S H.]]
+
[[Category: Lou Y]]
-
[[Category: Lou, Y.]]
+
[[Category: Shin DH]]
-
[[Category: Shin, D H.]]
+
[[Category: Yokota H]]
-
[[Category: Yokota, H.]]
+
-
[[Category: GDP]]
+
-
[[Category: ZN]]
+
-
[[Category: berkeley structural genomics center]]
+
-
[[Category: bsgc structure funded by nih]]
+
-
[[Category: gtpase]]
+
-
[[Category: ob-fold]]
+
-
[[Category: permutation]]
+
-
[[Category: protein structure initiative]]
+
-
[[Category: psi]]
+
-
[[Category: structural genomics]]
+
-
[[Category: zinc-finger]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:19:24 2008''
+

Current revision

Crystal structure of YjeQ from Thermotoga maritima

PDB ID 1u0l

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1u0l"
Personal tools