1t6d: Difference between revisions

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[[Image:1t6d.jpg|left|200px]]


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==MIRAS phasing of the Aquifex aeolicus Ppx/GppA phosphatase: crystal structure of the type II variant==
The line below this paragraph, containing "STRUCTURE_1t6d", creates the "Structure Box" on the page.
<StructureSection load='1t6d' size='340' side='right'caption='[[1t6d]], [[Resolution|resolution]] 2.15&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'>[[1t6d]] is a 2 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=1T6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6D 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]] 2.15&#8491;</td></tr>
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<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=CSX:S-OXY+CYSTEINE'>CSX</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
{{STRUCTURE_1t6d|  PDB=1t6d  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1t6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6d OCA], [https://pdbe.org/1t6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6d RCSB], [https://www.ebi.ac.uk/pdbsum/1t6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6d ProSAT]</span></td></tr>
 
</table>
'''MIRAS phasing of the Aquifex aeolicus Ppx/GppA phosphatase: crystal structure of the type II variant'''
== Function ==
 
[https://www.uniprot.org/uniprot/O67040_AQUAE O67040_AQUAE]  
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6d_consurf.spt"</scriptWhenChecked>
1T6D is a [[Single protein]] structure of sequence from [http://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=1T6D OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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://www.ncbi.nlm.nih.gov/pubmed/15248747 15248747]
</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=1t6d ConSurf].
[[Category: Aquifex aeolicus vf5]]
<div style="clear:both"></div>
[[Category: Single protein]]
__TOC__
[[Category: Gajhede, M.]]
</StructureSection>
[[Category: Kastrup, J S.]]
[[Category: Aquifex aeolicus VF5]]
[[Category: Kristensen, O.]]
[[Category: Large Structures]]
[[Category: Laurberg, M.]]
[[Category: Gajhede M]]
[[Category: Liljas, A.]]
[[Category: Kastrup JS]]
[[Category: Actin-like fold]]
[[Category: Kristensen O]]
[[Category: Alpha/beta protein]]
[[Category: Laurberg M]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 09:35:09 2008''
[[Category: Liljas A]]
Retrieved from "https://proteopedia.org/1t6d"