About: Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10.

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About: Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	The catalytic site of haloalkane dehalogenase DhlA is buried more than 10 A from the protein surface. While potential access channels to this site have been reported, the precise mechanism of substrate import and product export is still unconfirmed. We use computational methods to examine surface pockets and their putative roles in ligand access to and from the catalytic site. Computational solvent mapping moves small organic molecules %22probes%22 over the protein surface in order to identify energetically favorable sites, i.e., regions that tend to bind a variety of molecules. The mapping of three DhlA structures identifies seven such regions, some of which have been previously suggested to be involved in the binding and the import/export of substrates or products. These sites are the active site, the putative entrance of the channel leading to the active site, two pockets that bind Br- ions, a pocket in the slot region, and two additional sites between the main domain and the cap of DhlA. The catalytic site of haloalkane dehalogenase DhlA is buried more than 10 A from the protein surface. While potential access channels to this site have been reported, the precise mechanism of substrate import and product export is still unconfirmed. We use computational methods to examine surface pockets and their putative roles in ligand access to and from the catalytic site. Computational solvent mapping moves small organic molecules %22probes%22 over the protein surface in order to identify energetically favorable sites, i.e., regions that tend to bind a variety of molecules. The mapping of three DhlA structures identifies seven such regions, some of which have been previously suggested to be involved in the binding and the import/export of substrates or products. These sites are the active site, the putative entrance of the channel leading to the active site, two pockets that bind Br- ions, a pocket in the slot region, and two additional sites between the main domain and the cap of DhlA. (en)
Title	Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. (en)
skos:prefLabel	Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. (en)
skos:notation	RIV/00216224:14310/07:00022813!RIV10-MSM-14310___
http://linked.open...avai/riv/aktivita	P
http://linked.open...avai/riv/aktivity	P(LC06010)
http://linked.open...iv/cisloPeriodika	32
http://linked.open...vai/riv/dodaniDat	2010
http://linked.open...aciTvurceVysledku	Damborský, Jiří
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	421349
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/07:00022813
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	haloalkane dehalogenase DhlA; computational methods; catalytic site; DhlA structures; CAVER; LinB (en)
http://linked.open.../riv/klicoveSlovo	computational methods CAVER LinB DhlA structures catalytic site haloalkane dehalogenase DhlA
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[CE0D7A8A4B33]
http://linked.open...i/riv/nazevZdroje	Biochemistry
http://linked.open...in/vavai/riv/obor	CE
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	3 (xsd:int)
http://linked.open...vavai/riv/projekt	Center of Biocatalysis and Biotransformation
http://linked.open...UplatneniVysledku	2007
http://linked.open...v/svazekPeriodika	46
http://linked.open...iv/tvurceVysledku	Damborský, Jiří Silberstein, Michael Vajda, Sandor
http://linked.open...ain/vavai/riv/wos	000248728100009
issn	1520-4995
number of pages	10 (xsd:int)
http://localhost/t...ganizacniJednotka	14310
is http://linked.open...avai/riv/vysledek of	Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10.

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