This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2gja

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:28, 14 February 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2gja.gif|left|200px]]
 
-
<!--
+
==Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and NH4+==
-
The line below this paragraph, containing "STRUCTURE_2gja", creates the "Structure Box" on the page.
+
<StructureSection load='2gja' size='340' side='right'caption='[[2gja]], [[Resolution|resolution]] 1.85&Aring;' 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'>[[2gja]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GJA 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]] 1.85&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene></td></tr>
-
{{STRUCTURE_2gja| PDB=2gja | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gja OCA], [https://pdbe.org/2gja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gja RCSB], [https://www.ebi.ac.uk/pdbsum/2gja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gja ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and NH4+'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/MNME_ECOLI MNME_ECOLI] Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34.
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
MnmE, a Guanine nucleotide-binding protein conserved between bacteria and man, is involved in the modification of tRNAs. Here we provide biochemical and X-ray structural evidence for a new GTP-hydrolysis mechanism, where the G-domains of MnmE dimerise in a potassium-dependent manner and induce GTP hydrolysis. The structure in the presence of GDP-AlFx and potassium shows how juxtaposition of the subunits induces a conformational change around the nucleotide which reorients the catalytic machinery. A critical glutamate is positioned such as to stabilise or activate the attacking water. Potassium provides a positive charge into the catalytic site in a position analogous to the arginine finger in the Ras-RasGAP system. Mutational studies show that potassium-dependent dimerisation and GTP hydrolysis can be uncoupled and that interaction between the G-domains is a prerequisite for subsequent phosphoryl transfer. We propose a model for the juxtaposition of G-domains in the full-length protein and how it induces conformational changes in the putative tRNA-modification centre.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gj/2gja_consurf.spt"</scriptWhenChecked>
-
2GJA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GJA OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element., Scrima A, Wittinghofer A, EMBO J. 2006 Jun 21;25(12):2940-51. Epub 2006 Jun 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16763562 16763562]
+
</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=2gja ConSurf].
-
[[Category: Escherichia coli]]
+
<div style="clear:both"></div>
-
[[Category: Single protein]]
+
__TOC__
-
[[Category: Scrima, A.]]
+
</StructureSection>
-
[[Category: Wittinghofer, A.]]
+
[[Category: Large Structures]]
-
[[Category: Alpha-beta-sandwich]]
+
[[Category: Scrima A]]
-
[[Category: G-domain dimer]]
+
[[Category: Wittinghofer A]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 05:10:18 2008''
+

Current revision

Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and NH4+

PDB ID 2gja

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/2gja"
Personal tools