1rlo
From Proteopedia
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| - | [[Image:1rlo.jpg|left|200px]] | ||
| - | + | ==Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12== | |
| - | + | <StructureSection load='1rlo' size='340' side='right'caption='[[1rlo]], [[Resolution|resolution]] 2.00Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | | | + | <table><tr><td colspan='2'>[[1rlo]] 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=1RLO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RLO 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]] 2Å</td></tr> | |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1rlo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rlo OCA], [https://pdbe.org/1rlo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rlo RCSB], [https://www.ebi.ac.uk/pdbsum/1rlo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rlo ProSAT]</span></td></tr> | |
| - | + | </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/1rlo_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=1rlo ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
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. | 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. | ||
| - | + | 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:15657928<ref>PMID:15657928</ref> | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| + | <div class="pdbe-citations 1rlo" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: Lee | + | [[Category: Lee SY]] |
| - | [[Category: McCullagh | + | [[Category: McCullagh E]] |
| - | [[Category: Roberts | + | [[Category: Roberts A]] |
| - | [[Category: Silversmith | + | [[Category: Silversmith RE]] |
| - | [[Category: Wemmer | + | [[Category: Wemmer DE]] |
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Current revision
Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12
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