1t6c: Difference between revisions

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New page: left|200px<br /><applet load="1t6c" size="450" color="white" frame="true" align="right" spinBox="true" caption="1t6c, resolution 1.53Å" /> '''Structural character...
 
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[[Image:1t6c.jpg|left|200px]]<br /><applet load="1t6c" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1t6c, resolution 1.53&Aring;" />
'''Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member'''<br />


==Overview==
==Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member==
Exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA), enzymes play central roles in the bacterial stringent response induced by, starvation. The high-resolution crystal structure of the putative Aquifex, aeolicus PPX/GPPA phosphatase from the actin-like ATPase domain, superfamily has been determined, providing the first insights to features, of the common catalytic core of the PPX/GPPA family. The protein has a, two-domain structure with an active site located in the interdomain cleft., Two crystal forms were investigated (type I and II) at resolutions of 1.53, and 2.15 A, respectively. This revealed a structural flexibility that has, previously been described as a "butterfly-like" cleft opening around the, active site in other actin-like superfamily proteins. A calcium ion is, observed at the center of this region in type I crystals, substantiating, that PPX/GPPA enzymes use metal ions for catalysis. Structural analysis, suggests that nucleotides bind at a similar position to that seen in other, members of the superfamily.
<StructureSection load='1t6c' size='340' side='right'caption='[[1t6c]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1t6c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6C FirstGlance]. <br>
1T6C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5] with IOD, CA, CL and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1T6C 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]] 1.53&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=1t6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6c OCA], [https://pdbe.org/1t6c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6c RCSB], [https://www.ebi.ac.uk/pdbsum/1t6c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6c ProSAT]</span></td></tr>
Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family., Kristensen O, Laurberg M, Liljas A, Kastrup JS, Gajhede M, Biochemistry. 2004 Jul 20;43(28):8894-900. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15248747 15248747]
</table>
[[Category: Aquifex aeolicus vf5]]
== Function ==
[[Category: Single protein]]
[https://www.uniprot.org/uniprot/O67040_AQUAE O67040_AQUAE]  
[[Category: Gajhede, M.]]
== Evolutionary Conservation ==
[[Category: Kastrup, J.S.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Kristensen, O.]]
Check<jmol>
[[Category: Laurberg, M.]]
  <jmolCheckbox>
[[Category: Liljas, A.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6c_consurf.spt"</scriptWhenChecked>
[[Category: CA]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: CL]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: IOD]]
  </jmolCheckbox>
[[Category: MPD]]
</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=1t6c ConSurf].
[[Category: actin-like fold]]
<div style="clear:both"></div>
[[Category: alpha/beta protein]]
__TOC__
 
</StructureSection>
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:44:07 2007''
[[Category: Aquifex aeolicus VF5]]
[[Category: Large Structures]]
[[Category: Gajhede M]]
[[Category: Kastrup JS]]
[[Category: Kristensen O]]
[[Category: Laurberg M]]
[[Category: Liljas A]]

Latest revision as of 13:30, 13 March 2024

Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member

1t6c, resolution 1.53Å

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