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==Crystal structure of the amidase from geobacillus pallidus RAPc8== | |||
<StructureSection load='2plq' size='340' side='right'caption='[[2plq]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2plq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeribacillus_pallidus Aeribacillus pallidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PLQ 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]] 1.9Å</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=2plq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2plq OCA], [https://pdbe.org/2plq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2plq RCSB], [https://www.ebi.ac.uk/pdbsum/2plq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2plq ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/AMIE_BACSP AMIE_BACSP] Catalyzes the hydrolysis of short-chain aliphatic amides to their corresponding organic acids with release of ammonia.<ref>PMID:10978771</ref> Also exhibits in vitro acyl transferase activity, transferring the acyl moiety of short-chain amides to hydroxylamine to form hydroxamates (By similarity).<ref>PMID:10978771</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/pl/2plq_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=2plq ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 A resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4(2)32, with unit-cell parameter a = 130.49 (+/-0.05) A. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved. | The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 A resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4(2)32, with unit-cell parameter a = 130.49 (+/-0.05) A. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved. | ||
The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing.,Agarkar VB, Kimani SW, Cowan DA, Sayed MF, Sewell BT Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt, 12):1174-8. Epub 2006 Nov 4. PMID:17142891<ref>PMID:17142891</ref> | |||
The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing., Agarkar VB, Kimani SW, Cowan DA, Sayed MF, Sewell BT | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2plq" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Aeribacillus pallidus]] | |||
[[Category: Large Structures]] | |||
[[Category: Agarkar VB]] | |||
[[Category: Cowan DA]] | |||
[[Category: Kimani SW]] | |||
[[Category: Sayed MF]] | |||
[[Category: Sewell BT]] | |||
Latest revision as of 14:04, 30 August 2023
Crystal structure of the amidase from geobacillus pallidus RAPc8Crystal structure of the amidase from geobacillus pallidus RAPc8
Structural highlights
FunctionAMIE_BACSP Catalyzes the hydrolysis of short-chain aliphatic amides to their corresponding organic acids with release of ammonia.[1] Also exhibits in vitro acyl transferase activity, transferring the acyl moiety of short-chain amides to hydroxylamine to form hydroxamates (By similarity).[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 amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 A resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4(2)32, with unit-cell parameter a = 130.49 (+/-0.05) A. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved. The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing.,Agarkar VB, Kimani SW, Cowan DA, Sayed MF, Sewell BT Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt, 12):1174-8. Epub 2006 Nov 4. PMID:17142891[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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