Structure of an aliphatic amidase from Geobacillus pallidus RAPc8

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dc.contributor.authorKimani, S W
dc.contributor.authorAgarkar, V B
dc.contributor.authorCowan, D A
dc.contributor.authorSayed, M F.-R
dc.contributor.authorSewell, B T
dc.date.accessioned2016-07-28T15:20:28Z
dc.date.available2016-07-28T15:20:28Z
dc.date.issued2007
dc.date.updated2016-07-28T15:18:29Z
dc.description.abstractThe amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase superfamily and catalyzes the conversion of amides to the corresponding carboxylic acids and ammonia. It shows both amide-hydrolysis and acyl-transfer activities and also exhibits stereoselectivity for some enantiomeric substrates, thus making it a potentially important industrial catalyst. The crystal structure of G. pallidus RAPc8 amidase at a resolution of 1.9 Å was solved by molecular replacement from a crystal belonging to the primitive cubic space group P4232. G. pallidus RAPc8 amidase is homohexameric in solution and its monomers have the typical nitrilase-superfamily [alpha]-[beta]-[beta]-[alpha] fold. Association in the hexamer preserves the eight-layered [alpha]-[beta]-[beta]-[alpha]:[alpha]-[beta]-[beta]-[alpha] structure across an interface which is conserved in the known members of the superfamily. The extended carboxy-terminal tail contributes to this conserved interface by interlocking the monomers. Analysis of the small active site of the G. pallidus RAPc8 amidase suggests that access of a water molecule to the catalytic triad (Cys, Glu, Lys) side chains would be impeded by the formation of the acyl intermediate. It is proposed that another active-site residue, Glu142, the position of which is conserved in the homologues, acts as a general base to catalyse the hydrolysis of this intermediate. The small size of the substrate-binding pocket also explains the specificity of this enzyme for short aliphatic amides and its asymmetry explains its enantioselectivity.en_ZA
dc.identifierhttp://dx.doi.org/10.1107/S090744490703836X
dc.identifier.apacitationKimani, S. W., Agarkar, V. B., Cowan, D. A., Sayed, M F. -R., & Sewell, B. T. (2007). Structure of an aliphatic amidase from Geobacillus pallidus RAPc8. <i>Acta Crystallographica. Section D</i>, http://hdl.handle.net/11427/21005en_ZA
dc.identifier.chicagocitationKimani, S W, V B Agarkar, D A Cowan, M F.-R Sayed, and B T Sewell "Structure of an aliphatic amidase from Geobacillus pallidus RAPc8." <i>Acta Crystallographica. Section D</i> (2007) http://hdl.handle.net/11427/21005en_ZA
dc.identifier.citationKimani, S. W., Agarkar, V. B., Cowan, D. A., Sayed, M. R., & Sewell, B. T. (2007). Structure of an aliphatic amidase from Geobacillus pallidus RAPc8. Acta Crystallographica Section D: Biological Crystallography, 63(10), 1048-1058.en_ZA
dc.identifier.issn1048-1058en_ZA
dc.identifier.ris TY - Journal Article AU - Kimani, S W AU - Agarkar, V B AU - Cowan, D A AU - Sayed, M F.-R AU - Sewell, B T AB - The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase superfamily and catalyzes the conversion of amides to the corresponding carboxylic acids and ammonia. It shows both amide-hydrolysis and acyl-transfer activities and also exhibits stereoselectivity for some enantiomeric substrates, thus making it a potentially important industrial catalyst. The crystal structure of G. pallidus RAPc8 amidase at a resolution of 1.9 Å was solved by molecular replacement from a crystal belonging to the primitive cubic space group P4232. G. pallidus RAPc8 amidase is homohexameric in solution and its monomers have the typical nitrilase-superfamily [alpha]-[beta]-[beta]-[alpha] fold. Association in the hexamer preserves the eight-layered [alpha]-[beta]-[beta]-[alpha]:[alpha]-[beta]-[beta]-[alpha] structure across an interface which is conserved in the known members of the superfamily. The extended carboxy-terminal tail contributes to this conserved interface by interlocking the monomers. Analysis of the small active site of the G. pallidus RAPc8 amidase suggests that access of a water molecule to the catalytic triad (Cys, Glu, Lys) side chains would be impeded by the formation of the acyl intermediate. It is proposed that another active-site residue, Glu142, the position of which is conserved in the homologues, acts as a general base to catalyse the hydrolysis of this intermediate. The small size of the substrate-binding pocket also explains the specificity of this enzyme for short aliphatic amides and its asymmetry explains its enantioselectivity. DA - 2007 DB - OpenUCT DP - University of Cape Town J1 - Acta Crystallographica. Section D LK - https://open.uct.ac.za PB - University of Cape Town PY - 2007 SM - 1048-1058 T1 - Structure of an aliphatic amidase from Geobacillus pallidus RAPc8 TI - Structure of an aliphatic amidase from Geobacillus pallidus RAPc8 UR - http://hdl.handle.net/11427/21005 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/21005
dc.identifier.urihttp://scripts.iucr.org/cgi-bin/paper?S090744490703836X
dc.identifier.vancouvercitationKimani SW, Agarkar VB, Cowan DA, Sayed M F-R, Sewell BT. Structure of an aliphatic amidase from Geobacillus pallidus RAPc8. Acta Crystallographica. Section D. 2007; http://hdl.handle.net/11427/21005.en_ZA
dc.languageengen_ZA
dc.publisherInternational Union of Crystallographyen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.sourceActa Crystallographica. Section Den_ZA
dc.source.urihttp://journals.iucr.org/d/
dc.subject.otheramidases
dc.subject.otherAmiE
dc.subject.othernitrilases
dc.subject.otherGeobacillus pallidus RAPc8
dc.subject.otherthermophiles.
dc.titleStructure of an aliphatic amidase from Geobacillus pallidus RAPc8en_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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