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1t6d

From Proteopedia

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[[Image:1t6d.jpg|left|200px]]
 
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{{Structure
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==MIRAS phasing of the Aquifex aeolicus Ppx/GppA phosphatase: crystal structure of the type II variant==
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|PDB= 1t6d |SIZE=350|CAPTION= <scene name='initialview01'>1t6d</scene>, resolution 2.15&Aring;
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<StructureSection load='1t6d' size='340' side='right'caption='[[1t6d]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <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>
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<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>
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|ACTIVITY=
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</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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|GENE= ppx ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 Aquifex aeolicus VF5])
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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>
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|DOMAIN=
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<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>
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|RELATEDENTRY=[[1t6c|1T6C]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1t6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6d OCA], [http://www.ebi.ac.uk/pdbsum/1t6d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1t6d RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/O67040_AQUAE O67040_AQUAE]
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== Evolutionary Conservation ==
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'''MIRAS phasing of the Aquifex aeolicus Ppx/GppA phosphatase: crystal structure of the type II variant'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6d_consurf.spt"</scriptWhenChecked>
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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.
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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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].
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</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].
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<div style="clear:both"></div>
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==Reference==
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__TOC__
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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]
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</StructureSection>
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[[Category: Aquifex aeolicus vf5]]
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[[Category: Aquifex aeolicus VF5]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Gajhede, M.]]
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[[Category: Gajhede M]]
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[[Category: Kastrup, J S.]]
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[[Category: Kastrup JS]]
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[[Category: Kristensen, O.]]
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[[Category: Kristensen O]]
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[[Category: Laurberg, M.]]
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[[Category: Laurberg M]]
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[[Category: Liljas, A.]]
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[[Category: Liljas A]]
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[[Category: actin-like fold]]
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[[Category: alpha/beta protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:51:54 2008''
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Current revision

MIRAS phasing of the Aquifex aeolicus Ppx/GppA phosphatase: crystal structure of the type II variant

PDB ID 1t6d

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