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

J 2007

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

SILBERSTEIN, Michael, Jiří DAMBORSKÝ a Sandor VAJDA

Základní údaje

Originální název

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

Název česky

Výzkum vazebných míst haloalkan dehalogenázy DhlA z bakterie Xanthobacter autotrophicus GJ10.

Autoři

SILBERSTEIN, Michael (840 Spojené státy), Jiří DAMBORSKÝ (203 Česká republika, garant) a Sandor VAJDA (840 Spojené státy)

Vydání

Biochemistry, 2007, 1520-4995

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Kód RIV

RIV/00216224:14310/07:00022813

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000248728100009

Klíčová slova anglicky

haloalkane dehalogenase DhlA ; computational methods; catalytic site; DhlA structures ; CAVER; LinB

Štítky

catalytic site, CAVER, computational methods, DhlA structures, haloalkane dehalogenase DhlA, LINB

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 19. 3. 2010 12:25, prof. Mgr. Jiří Damborský, Dr.

Anotace

ORIG CZ

V originále

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 "probes" 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. We also performed mapping and free energy analysis of the DhlA structures using the substrate, 1,2-dichloroethane, and halide ions as probes. The findings were compared to crystallographic data and to results obtained by CAVER, a program developed for finding routes from protein clefts and cavities to the surface. Solvent mapping precisely reproduced all three Br- binding sites identified by protein crystallography and the openings to four channels found by CAVER. The analyses suggest that: (i) the active site has the highest affinity for the substrate molecule, (ii) the substrate initially binds at the entrance of the main tunnel, (iii) the site Br2, close to the entrance, is likely to serve as an intermediate binding site in product export, (iv) the site Br3, induced in the structure at high concentrations of Br-, could be part of an auxiliary route for product release and (v) three of the identified sites are likely to be entrances of water access channels leading to the active site. For comparison we also mapped haloalkane dehalogenases DhaA and LinB, both of which contain significantly larger and more solvent accessible binding sites than DhlA. The mapping of DhaA and LinB places the majority of probes in the active site, but most of the other six regions consistently identified in DhlA were not observed, suggesting that the more open active site eliminates the need for intermediate binding sites for the collision complex seen in DhlA.

Česky

xxx

Návaznosti

LC06010, projekt VaV

Název: Centrum biokatalýzy a biotransformací

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Centrum biokatalýzy a biotransformací

Citovat

SILBERSTEIN, Michael, Jiří DAMBORSKÝ a Sandor VAJDA. Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Biochemistry. 2007, roč. 46, č. 32, s. 9239-9249, 10 s. ISSN 1520-4995.

@article{727108,
   author = {Silberstein, Michael and Damborský, Jiří and Vajda, Sandor},
   article_number = {32},
   keywords = {haloalkane dehalogenase DhlA ; computational methods; catalytic site; DhlA structures ; CAVER; LinB},
   language = {eng},
   issn = {1520-4995},
   journal = {Biochemistry},
   title = {Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10.},
   url = {http://loschmidt.chemi.muni.cz/peg/abstracts/biochem07a.html},
   volume = {46},
   year = {2007}
}

TY  - JOUR
ID  - 727108
AU  - Silberstein, Michael - Damborský, Jiří - Vajda, Sandor
PY  - 2007
TI  - Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10.
JF  - Biochemistry
VL  - 46
IS  - 32
SP  - 9239-9249
EP  - 9239-9249
SN  - 15204995
KW  - haloalkane dehalogenase DhlA
KW  - computational methods
KW  - catalytic site
KW  - DhlA structures
KW  - CAVER
KW  - LinB
UR  - http://loschmidt.chemi.muni.cz/peg/abstracts/biochem07a.html
N2  - 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 "probes" 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. We also performed mapping and free energy analysis of the DhlA structures using the substrate, 1,2-dichloroethane, and halide ions as probes. The findings were compared to crystallographic data and to results obtained by CAVER, a program developed for finding routes from protein clefts and cavities to the surface. Solvent mapping precisely reproduced all three Br- binding sites identified by protein crystallography and the openings to four channels found by CAVER. The analyses suggest that: (i) the active site has the highest affinity for the substrate molecule, (ii) the substrate initially binds at the entrance of the main tunnel, (iii) the site Br2, close to the entrance, is likely to serve as an intermediate binding site in product export, (iv) the site Br3, induced in the structure at high concentrations of Br-, could be part of an auxiliary route for product release and (v) three of the identified sites are likely to be entrances of water access channels leading to the active site. For comparison we also mapped haloalkane dehalogenases DhaA and LinB, both of which contain significantly larger and more solvent accessible binding sites than DhlA. The mapping of DhaA and LinB places the majority of probes in the active site, but most of the other six regions consistently identified in DhlA were not observed, suggesting that the more open active site eliminates the need for intermediate binding sites for the collision complex seen in DhlA.
ER  -

SILBERSTEIN, Michael, Jiří DAMBORSKÝ a Sandor VAJDA. Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. \textit{Biochemistry}. 2007, roč.~46, č.~32, s.~9239-9249, 10 s. ISSN~1520-4995.

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