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| | ==Crystal structure of the amidase from geobacillus pallidus RAPc8== | | ==Crystal structure of the amidase from geobacillus pallidus RAPc8== |
| - | <StructureSection load='2plq' size='340' side='right' caption='[[2plq]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='2plq' size='340' side='right'caption='[[2plq]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2plq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51176 Atcc 51176]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PLQ FirstGlance]. <br> | + | <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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">amiE, ami ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33936 ATCC 51176])</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]] 1.9Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Amidase Amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.4 3.5.1.4] </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=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> |
| - | <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=2plq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2plq OCA], [http://pdbe.org/2plq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2plq RCSB], [http://www.ebi.ac.uk/pdbsum/2plq PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pl/2plq_consurf.spt"</scriptWhenChecked> | + | <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> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Amidase]] | + | [[Category: Aeribacillus pallidus]] |
| - | [[Category: Atcc 51176]] | + | [[Category: Large Structures]] |
| - | [[Category: Agarkar, V B]] | + | [[Category: Agarkar VB]] |
| - | [[Category: Cowan, D A]] | + | [[Category: Cowan DA]] |
| - | [[Category: Kimani, S W]] | + | [[Category: Kimani SW]] |
| - | [[Category: Sayed, M F]] | + | [[Category: Sayed MF]] |
| - | [[Category: Sewell, B T]] | + | [[Category: Sewell BT]] |
| - | [[Category: Alpha-beta-beta-alpha]]
| + | |
| - | [[Category: Hydrolase]]
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| - | [[Category: Nitrilase fold]]
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| Structural highlights
Function
AMIE_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 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 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
- ↑ Kim S, Oriel P. Cloning and expression of the nitrile hydratase and amidase genes from Bacillus sp. BR449 into Escherichia coli. Enzyme Microb Technol. 2000 Oct 1;27(7):492-501. PMID:10978771
- ↑ Kim S, Oriel P. Cloning and expression of the nitrile hydratase and amidase genes from Bacillus sp. BR449 into Escherichia coli. Enzyme Microb Technol. 2000 Oct 1;27(7):492-501. PMID:10978771
- ↑ Agarkar VB, Kimani SW, Cowan DA, Sayed MF, Sewell BT. The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt, 12):1174-8. Epub 2006 Nov 4. PMID:17142891 doi:10.1107/S1744309106043855
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