1o87

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:30, 13 December 2023) (edit) (undo)
 
(18 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1o87.gif|left|200px]]<br />
 
-
<applet load="1o87" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1o87, resolution 2.10&Aring;" />
 
-
'''A NEW MGGDP COMPLEX OF THE FFH NG DOMAIN'''<br />
 
-
==Overview==
+
==A new MgGDP complex of the Ffh NG domain==
-
Ffh is the signal sequence recognition and targeting subunit of the, prokaryotic signal recognition particle (SRP). Previous structural studies, of the NG GTPase domain of Ffh demonstrated magnesium-dependent and, magnesium-independent binding conformations for GDP and GMPPNP that are, believed to reflect novel mechanisms for exchange and activation in this, member of the GTPase superfamily. The current study of the NG GTPase bound, to Mg(2+)GDP reveals two new binding conformations-in the first the, magnesium interactions are similar to those seen previously, however, the, protein undergoes a conformational change that brings a conserved, aspartate into its second coordination sphere. In the second, the protein, conformation is similar to that seen previously, but the magnesium, coordination sphere is disrupted so that only five oxygen ligands are, present. The loss of the coordinating water molecule, at the position that, would be occupied by the oxygen of the gamma-phosphate of GTP, is, consistent with that position being privileged for exchange during, phosphate release. The available structures of the GDP-bound protein, provide a series of structural snapshots that illuminate steps along the, pathway of GDP release following GTP hydrolysis.
+
<StructureSection load='1o87' size='340' side='right'caption='[[1o87]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1o87]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O87 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]] 2.1&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1o87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o87 OCA], [https://pdbe.org/1o87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o87 RCSB], [https://www.ebi.ac.uk/pdbsum/1o87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o87 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/SRP54_THEAQ SRP54_THEAQ] Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY (By similarity).[HAMAP-Rule:MF_00306]
 +
== 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/o8/1o87_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=1o87 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Ffh is the signal sequence recognition and targeting subunit of the prokaryotic signal recognition particle (SRP). Previous structural studies of the NG GTPase domain of Ffh demonstrated magnesium-dependent and magnesium-independent binding conformations for GDP and GMPPNP that are believed to reflect novel mechanisms for exchange and activation in this member of the GTPase superfamily. The current study of the NG GTPase bound to Mg(2+)GDP reveals two new binding conformations-in the first the magnesium interactions are similar to those seen previously, however, the protein undergoes a conformational change that brings a conserved aspartate into its second coordination sphere. In the second, the protein conformation is similar to that seen previously, but the magnesium coordination sphere is disrupted so that only five oxygen ligands are present. The loss of the coordinating water molecule, at the position that would be occupied by the oxygen of the gamma-phosphate of GTP, is consistent with that position being privileged for exchange during phosphate release. The available structures of the GDP-bound protein provide a series of structural snapshots that illuminate steps along the pathway of GDP release following GTP hydrolysis.
-
==About this Structure==
+
Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh.,Focia PJ, Alam H, Lu T, Ramirez UD, Freymann DM Proteins. 2004 Feb 1;54(2):222-30. PMID:14696184<ref>PMID:14696184</ref>
-
1O87 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] with CL, MG, GDP and FMT as [http://en.wikipedia.org/wiki/ligands ligands]. Structure known Active Site: PLA. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1O87 OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh., Focia PJ, Alam H, Lu T, Ramirez UD, Freymann DM, Proteins. 2004 Feb 1;54(2):222-30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14696184 14696184]
+
</div>
-
[[Category: Single protein]]
+
<div class="pdbe-citations 1o87" style="background-color:#fffaf0;"></div>
-
[[Category: Thermus aquaticus]]
+
-
[[Category: Freymann, D.M.]]
+
-
[[Category: CL]]
+
-
[[Category: FMT]]
+
-
[[Category: GDP]]
+
-
[[Category: MG]]
+
-
[[Category: ffh]]
+
-
[[Category: gtp-binding]]
+
-
[[Category: gtpase]]
+
-
[[Category: rna-binding]]
+
-
[[Category: signal recognition particle]]
+
-
[[Category: srp]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 16:46:16 2007''
+
==See Also==
 +
*[[Signal recognition particle 3D structures|Signal recognition particle 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Thermus aquaticus]]
 +
[[Category: Freymann DM]]

Current revision

A new MgGDP complex of the Ffh NG domain

PDB ID 1o87

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/1o87"
Personal tools