2vqr: Difference between revisions

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-{{Seed}}
-[[Image:2vqr.jpg|left|200px]]
-<!--
+==Crystal structure of a phosphonate monoester hydrolase from rhizobium leguminosarum: a new member of the alkaline phosphatase superfamily==
-The line below this paragraph, containing "STRUCTURE_2vqr", creates the "Structure Box" on the page.
+<StructureSection load='2vqr' size='340' side='right'caption='[[2vqr]], [[Resolution|resolution]] 1.42&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'>[[2vqr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhil3 Rhil3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VQR FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDZ:3,3-DIHYDROXY+L-ALANINE'>DDZ</scene></td></tr>
-{{STRUCTURE_2vqr|  PDB=2vqr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vqr OCA], [https://pdbe.org/2vqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vqr RCSB], [https://www.ebi.ac.uk/pdbsum/2vqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vqr ProSAT]</span></td></tr>
+</table>
+== 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/vq/2vqr_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2vqr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The alkaline phosphatase superfamily comprises a large number of hydrolytic metalloenzymes such as phosphatases and sulfatases. We have characterised a new member of this superfamily, a phosphonate monoester hydrolase/phosphodiesterase from Rhizobium leguminosarum (R/PMH) both structurally and kinetically. The 1.42 A crystal structure shows structural homology to arylsulfatases with conservation of the core alpha/beta-fold, the mononuclear active site and most of the active-site residues. Sulfatases use a unique formylglycine nucleophile, formed by posttranslational modification of a cysteine/serine embedded in a signature sequence (C/S)XPXR. We provide mass spectrometric and mutational evidence that R/PMH is the first non-sulfatase enzyme shown to use a formylglycine as the catalytic nucleophile. R/PMH hydrolyses phosphonate monoesters and phosphate diesters with similar efficiency. Burst kinetics suggest that substrate hydrolysis proceeds via a double-displacement mechanism. Kinetic characterisation of active-site mutations establishes the catalytic contributions of individual residues. A mechanism for substrate hydrolysis is proposed on the basis of the kinetic data and structural comparisons with E. coli alkaline phosphatase and Pseudomonas aeruginosa arylsulfatase. R/PMH represents a further example of conservation of the overall structure and mechanism within the alkaline phosphatase superfamily.
-===CRYSTAL STRUCTURE OF A PHOSPHONATE MONOESTER HYDROLASE FROM RHIZOBIUM LEGUMINOSARUM: A NEW MEMBER OF THE ALKALINE PHOSPHATASE SUPERFAMILY===
+A new member of the alkaline phosphatase superfamily with a formylglycine nucleophile: structural and kinetic characterisation of a phosphonate monoester hydrolase/phosphodiesterase from Rhizobium leguminosarum.,Jonas S, van Loo B, Hyvonen M, Hollfelder F J Mol Biol. 2008 Dec 5;384(1):120-36. Epub 2008 Sep 4. PMID:18793651<ref>PMID:18793651</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18793651}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vqr" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18793651 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18793651}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VQR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhizobium_leguminosarum_bv._viciae Rhizobium leguminosarum bv. viciae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VQR OCA].
+[[Category: Rhil3]]
+[[Category: Hollfelder, F]]
-==Reference==
+[[Category: Hyvonen, M]]
-A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium leguminosarum., Jonas S, van Loo B, Hyvonen M, Hollfelder F, J Mol Biol. 2008 Sep 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18793651 18793651]
+[[Category: Jonas, S]]
-[[Category: Rhizobium leguminosarum bv. viciae]]
-[[Category: Single protein]]
-[[Category: Hollfelder, F.]]
-[[Category: Hyvonen, M.]]
-[[Category: Jonas, S.]]
 [[Category: Alkaline phosphatase superfamily]]
 [[Category: Formylglycine]]
@@ Line 35: / Line 42: @@
 [[Category: Phosphonate monoester hydrolase]]
 [[Category: Plasmid]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct  1 21:36:42 2008''