1ypp

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[[Image:1ypp.gif|left|200px]]<br /><applet load="1ypp" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ypp, resolution 2.4&Aring;" />
 
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'''ACID ANHYDRIDE HYDROLASE'''<br />
 
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==Overview==
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==ACID ANHYDRIDE HYDROLASE==
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The three-dimensional structure of the manganese-phosphate complex of inorganic pyrophosphatase from Saccharomyces cerevisiae has been refined to an R factor of 19.0% at 2.4-A resolution. X-ray data were collected from a single crystal using an imaging plate scanner and synchrotron radiation. There is one dimeric molecule in the asymmetric unit. The upper estimate of the root-mean-square coordinate error is 0.4 A using either the delta A plot or the superposition of the two crystallographically independent subunits. The good agreement between the coordinates of the two subunits, which were not subjected to non-crystallographic symmetry restraints, provides independent validation of the structure analysis. The active site in each subunit contains four manganese ions and two phosphates. The manganese ions are coordinated by the side chains of aspartate and glutamate residues. The phosphate groups, which were identified on the basis of their local stereochemistry, interact either directly or via water molecules with manganese ions and lysine, arginine, and tyrosine side chains. The phosphates are bridged by two of the manganese ions. The outer phosphate is exposed to solvent. The inner phosphate is surrounded by all four manganese ions. The ion-binding sites are related to the order of binding previously established from kinetic studies. A hypothesis for the transition state of the catalytic reaction is put forward.
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<StructureSection load='1ypp' size='340' side='right'caption='[[1ypp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ypp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YPP FirstGlance]. <br>
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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]] 2.4&#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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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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=1ypp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ypp OCA], [https://pdbe.org/1ypp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ypp RCSB], [https://www.ebi.ac.uk/pdbsum/1ypp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ypp ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/IPYR_YEAST IPYR_YEAST]
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== Evolutionary Conservation ==
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yp/1ypp_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=1ypp ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1YPP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=MN:'>MN</scene> and <scene name='pdbligand=PO4:'>PO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YPP OCA].
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*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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X-ray structure of yeast inorganic pyrophosphatase complexed with manganese and phosphate., Harutyunyan EH, Kuranova IP, Vainshtein BK, Hohne WE, Lamzin VS, Dauter Z, Teplyakov AV, Wilson KS, Eur J Biochem. 1996 Jul 1;239(1):220-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8706712 8706712]
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[[Category: Large Structures]]
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[[Category: Inorganic diphosphatase]]
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Dauter Z]]
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[[Category: Dauter, Z.]]
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[[Category: Harutyunyan EH]]
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[[Category: Harutyunyan, E H.]]
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[[Category: Kuranova IP]]
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[[Category: Kuranova, I P.]]
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[[Category: Lamzin VS]]
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[[Category: Lamzin, V S.]]
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[[Category: Wilson KS]]
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[[Category: Wilson, K S.]]
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[[Category: MN]]
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[[Category: PO4]]
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[[Category: hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:07:50 2008''
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Current revision

ACID ANHYDRIDE HYDROLASE

PDB ID 1ypp

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