2b82: Difference between revisions
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< | ==Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate bound to the catalytic metal at 1.2 A resolution== | ||
<StructureSection load='2b82' size='340' side='right'caption='[[2b82]], [[Resolution|resolution]] 1.25Å' scene=''> | |||
== Structural highlights == | |||
or the | <table><tr><td colspan='2'>[[2b82]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rmw 1rmw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B82 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B82 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]] 1.25Å</td></tr> | |||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2b82 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b82 OCA], [https://pdbe.org/2b82 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b82 RCSB], [https://www.ebi.ac.uk/pdbsum/2b82 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b82 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/APHA_ECOLI APHA_ECOLI] Dephosphorylates several organic phosphate monoesters including 3'- and 5'-nucleotides, 2'-deoxy-5'-nucleotides, pNPP, phenyl phosphate, glycerol 2-phosphate, ribose 5-phosphate, O-phospho-L-amino acids and phytic acid, showing the highest activity with aryl phosphoesters (pNPP, phenyl phosphate and O-phospho-L-tyrosine), and to a lesser extent with 3'- and 5'-nucleotides. No activity toward ATP, phosphodiesters, glycerol-1-phosphate, glucose 1-phosphate, glucose 6-phosphate, NADP, GTP or 3',5'-cAMP, ADP or ATP. Also has a phosphotransferase activity catalyzing the transfer of low-energy phosphate groups from organic phosphate monoesters to free hydroxyl groups of various organic compounds. Capable of transferring phosphate from either pNPP or UMP to adenosine or uridine. Does not exhibit nucleotide phosphomutase activity.<ref>PMID:9011040</ref> <ref>PMID:16297670</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/b8/2b82_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=2b82 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The Escherichia coli gene aphA codes for a periplasmic acid phosphatase called AphA, belonging to class B bacterial phosphatases, which is part of the DDDD superfamily of phosphohydrolases. After our first report about its crystal structure, we have started a series of crystallographic studies aimed at understanding of the catalytic mechanism of the enzyme. Here, we report three crystal structures of the AphA enzyme in complex with the hydrolysis products of nucleoside monophosphate substrates and a fourth with a proposed intermediate analogue that appears to be covalently bound to the enzyme. Comparison with the native enzyme structure and with the available X-ray structures of different phosphatases provides clues about the enzyme chemistry and allows us to propose a catalytic mechanism for AphA, and to discuss it with respect to the mechanism of other bacterial and human phosphatases. | |||
A structure-based proposal for the catalytic mechanism of the bacterial acid phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases.,Calderone V, Forleo C, Benvenuti M, Thaller MC, Rossolini GM, Mangani S J Mol Biol. 2006 Jan 27;355(4):708-21. Epub 2005 Nov 10. PMID:16330049<ref>PMID:16330049</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2b82" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Acid phosphatase 3D structures|Acid phosphatase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Benvenuti | [[Category: Benvenuti M]] | ||
[[Category: Calderone | [[Category: Calderone V]] | ||
[[Category: Forleo | [[Category: Forleo C]] | ||
[[Category: Mangani | [[Category: Mangani S]] | ||
[[Category: Rossolini | [[Category: Rossolini GM]] | ||
[[Category: Thaller | [[Category: Thaller MC]] | ||
Latest revision as of 10:35, 23 August 2023
Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate bound to the catalytic metal at 1.2 A resolutionCrystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate bound to the catalytic metal at 1.2 A resolution
Structural highlights
FunctionAPHA_ECOLI Dephosphorylates several organic phosphate monoesters including 3'- and 5'-nucleotides, 2'-deoxy-5'-nucleotides, pNPP, phenyl phosphate, glycerol 2-phosphate, ribose 5-phosphate, O-phospho-L-amino acids and phytic acid, showing the highest activity with aryl phosphoesters (pNPP, phenyl phosphate and O-phospho-L-tyrosine), and to a lesser extent with 3'- and 5'-nucleotides. No activity toward ATP, phosphodiesters, glycerol-1-phosphate, glucose 1-phosphate, glucose 6-phosphate, NADP, GTP or 3',5'-cAMP, ADP or ATP. Also has a phosphotransferase activity catalyzing the transfer of low-energy phosphate groups from organic phosphate monoesters to free hydroxyl groups of various organic compounds. Capable of transferring phosphate from either pNPP or UMP to adenosine or uridine. Does not exhibit nucleotide phosphomutase activity.[1] [2] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe Escherichia coli gene aphA codes for a periplasmic acid phosphatase called AphA, belonging to class B bacterial phosphatases, which is part of the DDDD superfamily of phosphohydrolases. After our first report about its crystal structure, we have started a series of crystallographic studies aimed at understanding of the catalytic mechanism of the enzyme. Here, we report three crystal structures of the AphA enzyme in complex with the hydrolysis products of nucleoside monophosphate substrates and a fourth with a proposed intermediate analogue that appears to be covalently bound to the enzyme. Comparison with the native enzyme structure and with the available X-ray structures of different phosphatases provides clues about the enzyme chemistry and allows us to propose a catalytic mechanism for AphA, and to discuss it with respect to the mechanism of other bacterial and human phosphatases. A structure-based proposal for the catalytic mechanism of the bacterial acid phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases.,Calderone V, Forleo C, Benvenuti M, Thaller MC, Rossolini GM, Mangani S J Mol Biol. 2006 Jan 27;355(4):708-21. Epub 2005 Nov 10. PMID:16330049[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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