2qfr

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of red kidney bean purple acid phosphatase with bound sulfate

Structural highlights

2qfr is a 2 chain structure with sequence from Phaseolus vulgaris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PPAF_PHAVU

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

BACKGROUND: Purple acid phosphatases belong to the family of binuclear metallohydrolases and are involved in a multitude of biological functions, ranging from bacterial killing and bone metabolism in animals to phosphate uptake in plants. Due to its role in bone resorption purple acid phosphatase has evolved into a promising target for the development of anti-osteoporotic chemotherapeutics. The design of specific and potent inhibitors for this enzyme is aided by detailed knowledge of its reaction mechanism. However, despite considerable effort in the last 10 years various aspects of the basic molecular mechanism of action are still not fully understood. RESULTS: Red kidney bean purple acid phosphatase is a heterovalent enzyme with an Fe(III)Zn(II) center in the active site. Two new structures with bound sulfate (2.4 A) and fluoride (2.2 A) provide insight into the pre-catalytic phase of its reaction cycle and phosphorolysis. The sulfate-bound structure illustrates the significance of an extensive hydrogen bonding network in the second coordination sphere in initial substrate binding and orientation prior to hydrolysis. Importantly, both metal ions are five-coordinate in this structure, with only one nucleophilic mu-hydroxide present in the metal-bridging position. The fluoride-bound structure provides visual support for an activation mechanism for this mu-hydroxide whereby substrate binding induces a shift of this bridging ligand towards the divalent metal ion, thus increasing its nucleophilicity. CONCLUSION: In combination with kinetic, crystallographic and spectroscopic data these structures of red kidney bean purple acid phosphatase facilitate the proposal of a comprehensive eight-step model for the catalytic mechanism of purple acid phosphatases in general.

Crystal structures of a purple acid phosphatase, representing different steps of this enzyme's catalytic cycle.,Schenk G, Elliott TW, Leung E, Carrington LE, Mitic N, Gahan LR, Guddat LW BMC Struct Biol. 2008 Jan 31;8:6. PMID:18234116^[1]

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

References

↑ Schenk G, Elliott TW, Leung E, Carrington LE, Mitic N, Gahan LR, Guddat LW. Crystal structures of a purple acid phosphatase, representing different steps of this enzyme's catalytic cycle. BMC Struct Biol. 2008 Jan 31;8:6. PMID:18234116 doi:10.1186/1472-6807-8-6

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/2qfr"

@@ Line 3: / Line 3: @@
 <StructureSection load='2qfr' size='340' side='right'caption='[[2qfr]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qfr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Phaseolus_vulgaris Phaseolus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2QFR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qfr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phaseolus_vulgaris Phaseolus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QFR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kbp|3kbp]], [[4kbp|4kbp]], [[2qfp|2qfp]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=2qfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfr OCA], [https://pdbe.org/2qfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qfr RCSB], [https://www.ebi.ac.uk/pdbsum/2qfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfr 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=2qfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfr OCA], [http://pdbe.org/2qfr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qfr RCSB], [http://www.ebi.ac.uk/pdbsum/2qfr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfr ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PPAF_PHAVU PPAF_PHAVU]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qf/2qfr_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Acid phosphatase]]
 [[Category: Large Structures]]
 [[Category: Phaseolus vulgaris]]
-[[Category: Elliot, T W]]
+[[Category: Elliot TW]]
-[[Category: Gahan, L R]]
+[[Category: Gahan LR]]
-[[Category: Guddat, L W]]
+[[Category: Guddat LW]]
-[[Category: Leung, E]]
+[[Category: Leung E]]
-[[Category: Schenk, G]]
+[[Category: Schenk G]]
-[[Category: Binuclear metal centre]]
-[[Category: Hydrolase]]
-[[Category: Substrate analog]]

2qfr

From Proteopedia

Current revision

Crystal structure of red kidney bean purple acid phosphatase with bound sulfate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox