1n9k

From Proteopedia

(Difference between revisions)

Revision as of 08:47, 2 December 2020

Crystal structure of the bromide adduct of AphA class B acid phosphatase/phosphotransferase from E. coli at 2.2 A resolution

Structural highlights

1n9k is a 2 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1n8n
Gene:	APHA ("Bacillus coli" Migula 1895)
Activity:	Acid phosphatase, with EC number 3.1.3.2
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

AphA is a periplasmic acid phosphatase of Escherichia coli belonging to class B bacterial phosphatases, which is part of the DDDD superfamily of phosphohydrolases. The crystal structure of AphA has been determined at 2.2A and its resolution extended to 1.7A on an AuCl(3) derivative. This represents the first crystal structure of a class B bacterial phosphatase. Despite the lack of sequence homology, the AphA structure reveals a haloacid dehalogenase-like fold. This finding suggests that this fold could be conserved among members of the DDDD superfamily of phosphohydrolases. The active enzyme is a homotetramer built by using an extended N-terminal arm intertwining the four monomers. The active site of the native enzyme, as prepared, hosts a magnesium ion, which can be replaced by other metal ions. The structure explains the non-specific behaviour of AphA towards substrates, while a structure-based alignment with other phosphatases provides clues about the catalytic mechanism.

The first structure of a bacterial class B Acid phosphatase reveals further structural heterogeneity among phosphatases of the haloacid dehalogenase fold.,Calderone V, Forleo C, Benvenuti M, Cristina Thaller M, Maria Rossolini G, Mangani S J Mol Biol. 2004 Jan 16;335(3):761-73. PMID:14687572^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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, Cristina Thaller M, Maria Rossolini G, Mangani S. The first structure of a bacterial class B Acid phosphatase reveals further structural heterogeneity among phosphatases of the haloacid dehalogenase fold. J Mol Biol. 2004 Jan 16;335(3):761-73. PMID:14687572

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1n9k"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the bromide adduct of AphA class B acid phosphatase/phosphotransferase from E. coli at 2.2 A resolution==
-<StructureSection load='1n9k' size='340' side='right' caption='[[1n9k]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='1n9k' size='340' side='right'caption='[[1n9k]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1n9k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N9K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N9K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1n9k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N9K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1N9K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1n8n|1n8n]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1n8n|1n8n]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APHA ([http://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'>[http://en.wikipedia.org/wiki/Acid_phosphatase Acid phosphatase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n9k OCA], [http://pdbe.org/1n9k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n9k RCSB], [http://www.ebi.ac.uk/pdbsum/1n9k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n9k ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1n9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n9k OCA], [http://pdbe.org/1n9k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n9k RCSB], [http://www.ebi.ac.uk/pdbsum/1n9k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n9k ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 16: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n9/1n9k_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n9/1n9k_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 31: @@
 </div>
 <div class="pdbe-citations 1n9k" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Acid phosphatase 3D structures|Acid phosphatase 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 40: @@
 [[Category: Bacillus coli migula 1895]]
 [[Category: Acid phosphatase]]
+[[Category: Large Structures]]
 [[Category: Benvenuti, M]]
 [[Category: Calderone, V]]

1n9k

From Proteopedia

Revision as of 08:47, 2 December 2020

Crystal structure of the bromide adduct of AphA class B acid phosphatase/phosphotransferase from E. coli at 2.2 A resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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