|
|
| Line 3: |
Line 3: |
| | <StructureSection load='2b8j' size='340' side='right'caption='[[2b8j]], [[Resolution|resolution]] 2.03Å' scene=''> | | <StructureSection load='2b8j' size='340' side='right'caption='[[2b8j]], [[Resolution|resolution]] 2.03Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2b8j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm7 1rm7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B8J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B8J FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2b8j]] 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=1rm7 1rm7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B8J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B8J FirstGlance]. <br> |
| - | </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=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=AU3:GOLD+3++ION'>AU3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.033Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b82|2b82]], [[1n8n|1n8n]], [[1n9k|1n9k]]</div></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=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=AU3:GOLD+3++ION'>AU3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aphA, napA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Acid_phosphatase Acid phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.2 3.1.3.2] </span></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=2b8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b8j OCA], [https://pdbe.org/2b8j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b8j RCSB], [https://www.ebi.ac.uk/pdbsum/2b8j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b8j ProSAT]</span></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=2b8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b8j OCA], [https://pdbe.org/2b8j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b8j RCSB], [https://www.ebi.ac.uk/pdbsum/2b8j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b8j ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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>
| + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 38: |
Line 36: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Acid phosphatase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Benvenuti, M]] | + | [[Category: Benvenuti M]] |
| - | [[Category: Calderone, V]] | + | [[Category: Calderone V]] |
| - | [[Category: Forleo, C]] | + | [[Category: Forleo C]] |
| - | [[Category: Mangani, S]] | + | [[Category: Mangani S]] |
| - | [[Category: Rossolini, G M]] | + | [[Category: Rossolini GM]] |
| - | [[Category: Thaller, M C]] | + | [[Category: Thaller MC]] |
| - | [[Category: Amp]]
| + | |
| - | [[Category: Class b acid phosphatase]]
| + | |
| - | [[Category: Dddd acid phosphatase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metallo-enzyme]]
| + | |
| Structural highlights
2b8j is a 2 chain structure with sequence from Escherichia coli. This structure supersedes the now removed PDB entry 1rm7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.033Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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.[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 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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Thaller MC, Schippa S, Bonci A, Cresti S, Rossolini GM. Identification of the gene (aphA) encoding the class B acid phosphatase/phosphotransferase of Escherichia coli MG1655 and characterization of its product. FEMS Microbiol Lett. 1997 Jan 15;146(2):191-8. PMID:9011040
- ↑ Passariello C, Forleo C, Micheli V, Schippa S, Leone R, Mangani S, Thaller MC, Rossolini GM. Biochemical characterization of the class B acid phosphatase (AphA) of Escherichia coli MG1655. Biochim Biophys Acta. 2006 Jan;1764(1):13-9. Epub 2005 Nov 2. PMID:16297670 doi:http://dx.doi.org/10.1016/j.bbapap.2005.08.028
- ↑ Calderone V, Forleo C, Benvenuti M, Thaller MC, Rossolini GM, Mangani S. A structure-based proposal for the catalytic mechanism of the bacterial acid phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases. J Mol Biol. 2006 Jan 27;355(4):708-21. Epub 2005 Nov 10. PMID:16330049 doi:http://dx.doi.org/10.1016/j.jmb.2005.10.068
|
