4kbp: Difference between revisions

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-[[Image:4kbp.gif|left|200px]]<br />
-<applet load="4kbp" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="4kbp, resolution 2.7&Aring;" />
-'''KIDNEY BEAN PURPLE ACID PHOSPHATASE'''<br />
-==Overview==
+==KIDNEY BEAN PURPLE ACID PHOSPHATASE==
-Purple acid phosphatase is a widely distributed non-specific, phosphomonoesterase. X-ray structures of the dimeric 111-kDa, Fe(III)-Zn(II) kidney bean purple acid phosphatase (kbPAP) complexed with, phosphate, the product of the reaction, and with tungstate, a strong, inhibitor of the phosphatase activity, were determined at 2.7 and 3.0, angstroms resolution, respectively. Furthermore the resolution of the, unligated enzyme, recently solved at 2.9 angstroms could be extended to, 2.65 angstroms with completely new data. The binding of both oxoanions is, not accompanied by larger conformational changes in the enzyme structure., Small movements with a maximal coordinate shift of 1 angstroms are only, observed for the active site residues His295 and His296. In the inhibitor, complex as well as in the product complex, the oxoanion binds in a, bidentate bridging mode to the two metal ions, replacing two of the, presumed solvent ligands present in the unligated enzyme form. As also, proposed for the unligated structure a bridging hydroxide ion completes, the coordination spheres of both metal ions to octahedral arrangements., All three structures reported herein support a mechanism of phosphate, ester hydrolysis involving interaction of the substrate with Zn(II), followed by a nucleophilic attack on the phosphorus by an, Fe(III)-coordinated hydroxide ion. The negative charge evolving at the, pentacoordinated transition state is probably stabilized by interactions, with the divalent zinc and the imidazole groups of His202, His295, and, His296, the latter protonating the leaving alcohol group.
+<StructureSection load='4kbp' size='340' side='right'caption='[[4kbp]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4kbp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Phaseolus_vulgaris Phaseolus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KBP 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]] 2.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4kbp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kbp OCA], [https://pdbe.org/4kbp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kbp RCSB], [https://www.ebi.ac.uk/pdbsum/4kbp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kbp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PPAF_PHAVU PPAF_PHAVU]
+== 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/kb/4kbp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=4kbp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Purple acid phosphatase is a widely distributed non-specific phosphomonoesterase. X-ray structures of the dimeric 111-kDa Fe(III)-Zn(II) kidney bean purple acid phosphatase (kbPAP) complexed with phosphate, the product of the reaction, and with tungstate, a strong inhibitor of the phosphatase activity, were determined at 2.7 and 3.0 angstroms resolution, respectively. Furthermore the resolution of the unligated enzyme, recently solved at 2.9 angstroms could be extended to 2.65 angstroms with completely new data. The binding of both oxoanions is not accompanied by larger conformational changes in the enzyme structure. Small movements with a maximal coordinate shift of 1 angstroms are only observed for the active site residues His295 and His296. In the inhibitor complex as well as in the product complex, the oxoanion binds in a bidentate bridging mode to the two metal ions, replacing two of the presumed solvent ligands present in the unligated enzyme form. As also proposed for the unligated structure a bridging hydroxide ion completes the coordination spheres of both metal ions to octahedral arrangements. All three structures reported herein support a mechanism of phosphate ester hydrolysis involving interaction of the substrate with Zn(II) followed by a nucleophilic attack on the phosphorus by an Fe(III)-coordinated hydroxide ion. The negative charge evolving at the pentacoordinated transition state is probably stabilized by interactions with the divalent zinc and the imidazole groups of His202, His295, and His296, the latter protonating the leaving alcohol group.
-==About this Structure==
+Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures.,Klabunde T, Strater N, Frohlich R, Witzel H, Krebs B J Mol Biol. 1996 Jun 21;259(4):737-48. PMID:8683579<ref>PMID:8683579</ref>
-KBP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Phaseolus_vulgaris Phaseolus vulgaris] with NAG, FE, ZN and PO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Acid_phosphatase Acid phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.2 3.1.3.2] Structure known Active Sites: ACA, ACB, ACC and ACD. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=4KBP OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures., Klabunde T, Strater N, Frohlich R, Witzel H, Krebs B, J Mol Biol. 1996 Jun 21;259(4):737-48. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8683579 8683579]
+</div>
-[[Category: Acid phosphatase]]
+<div class="pdbe-citations 4kbp" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Acid phosphatase 3D structures|Acid phosphatase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Phaseolus vulgaris]]
-[[Category: Single protein]]
+[[Category: Klabunde T]]
-[[Category: Klabunde, T.]]
+[[Category: Krebs B]]
-[[Category: Krebs, B.]]
+[[Category: Strater N]]
-[[Category: Strater, N.]]
-[[Category: FE]]
-[[Category: NAG]]
-[[Category: PO4]]
-[[Category: ZN]]
-[[Category: hydrolase (phosphoric monoester)]]
-[[Category: purple acid phosphatase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov  5 18:48:57 2007''