1rlm: Difference between revisions

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-[[Image:1rlm.jpg|left|200px]]<br /><applet load="1rlm" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1rlm, resolution 1.90&Aring;" />
-'''Crystal Structure of ybiV from Escherichia coli K12'''<br />
-==Overview==
+==Crystal Structure of ybiV from Escherichia coli K12==
-The protein YbiV from Escherichia coli K12 MG1655 is a hypothetical protein with sequence homology to the haloacid dehalogenase (HAD) superfamily of proteins. Although numerous members of this family have been identified, the functions of few are known. Using the crystal structure, sequence analysis, and biochemical assays, we have characterized YbiV as a HAD phosphatase. The crystal structure of YbiV reveals a two-domain protein, one with the characteristic HAD hydrolase fold, the other an inserted alpha/beta fold. In an effort to understand the mechanism, we also solved and report the structures of YbiV in complex with beryllofluoride (BeF3-) and aluminum trifluoride (AlF3), which have been shown to mimic the phosphorylated intermediate and transition state for hydrolysis, respectively, in analogy to other HAD phosphatases. Analysis of the structures reveals the substrate-binding cavity, which is hydrophilic in nature. Both structure and sequence homology indicate YbiV may be a sugar phosphatase, which is supported by biochemical assays that measured the release of free phosphate on a number of sugar-like substrates. We also investigated available genomic and functional data in an effort to determine the physiological substrate.
+<StructureSection load='1rlm' size='340' side='right'caption='[[1rlm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1rlm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RLM FirstGlance]. <br>
-RLM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RLM OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rlm OCA], [https://pdbe.org/1rlm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rlm RCSB], [https://www.ebi.ac.uk/pdbsum/1rlm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rlm ProSAT]</span></td></tr>
-YbiV from Escherichia coli K12 is a HAD phosphatase., Roberts A, Lee SY, McCullagh E, Silversmith RE, Wemmer DE, Proteins. 2005 Mar 1;58(4):790-801. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15657928 15657928]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SUPH_ECOLI SUPH_ECOLI] Catalyzes the hydrolysis of sugar phosphate to sugar and inorganic phosphate. Has a wide substrate specificity catalyzing the hydrolysis of ribose-5-phosphate, glucose-6-phosphate, fructose-1-phosphate, acetyl-phosphate, glycerol-1-phosphate, glycerol-2-phosphate, 2-deoxy-glucose-6-phosphate, mannose-6-phosphate and fructose-6-phosphate. Appears to have a low level of phosphotransferase activity using monophosphates as the phosphate donor.<ref>PMID:15808744</ref> <ref>PMID:16990279</ref> <ref>PMID:15657928</ref>
+== 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/rl/1rlm_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=1rlm ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Lee, S Y.]]
+[[Category: Lee SY]]
-[[Category: McCullagh, E.]]
+[[Category: McCullagh E]]
-[[Category: Roberts, A.]]
+[[Category: Roberts A]]
-[[Category: Silversmith, R E.]]
+[[Category: Silversmith RE]]
-[[Category: Wemmer, D E.]]
+[[Category: Wemmer DE]]
-[[Category: GOL]]
-[[Category: MG]]
-[[Category: had family]]
-[[Category: phosphatase]]
-[[Category: rossman fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:52:12 2008''