Quantitative Analysis of Substrate Specificity of Haloalkane
Dehalogenase LinB from Sphingomonas paucimobilis UT26

J 2005

Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26

KMUNÍČEK, Jan, Kamila HYNKOVÁ, Tomáš JEDLIČKA, Yuji NAGATA, Ana NEGRI et. al.

Basic information

Original name

Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26

Name in Czech

Kavntitativní analýza substrátové specifity haloalkan dehalogenazy LinB z bakterie Sphingomonas Paucimobilis UT26

Authors

KMUNÍČEK, Jan (203 Czech Republic), Kamila HYNKOVÁ (203 Czech Republic), Tomáš JEDLIČKA (203 Czech Republic), Yuji NAGATA (392 Japan), Ana NEGRI (724 Spain), Frederico GAGO (724 Spain), Rebecca WADE (276 Germany) and Jiří DAMBORSKÝ (203 Czech Republic, guarantor)

Edition

Biochemistry, 2005, 0006-2960

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.848

RIV identification code

RIV/00216224:14310/05:00013637

Organization unit

Faculty of Science

UT WoS

000227418500028

Keywords in English

Haloalkane dehalogenases; Quantitative Structure-Activity Relationships (QSAR); Sphingomonas paucimobilis UT26

Abstract

ORIG CZ

V originále

Haloalkane dehalogenases are microbial enzymes that cleave a carbon-halogen bond in halogenated compounds. The haloalkane dehalogenase LinB, isolated from Sphingomonas paucimobilis UT26, is a broad-specificity enzyme. Fifty five halogenated aliphatic and cyclic hydrocarbons were tested for dehalogenation with the LinB enzyme. The compounds for testing were systematically selected using a statistical experimental design. Steady-state kinetic constants Km and kcat were determined for twenty five substrates that showed detectable cleavage by the enzyme and low abiotic hydrolysis. Classical Quantitative Structure-Activity Relationships (QSAR) were used to correlate the kinetic constants with molecular descriptors and resulted in a model that explained 94% of experimental data variability. The binding affinity of the tested substrates for this haloalkane dehalogenase correlated with hydrophobicity, molecular surface, dipole moment and volume/surface ratio. Binding of the substrate molecules in the active site pocket of LinB depends non-linearly on the size of the molecules. Binding affinity increases with increasing substrate size up to a chain length of six carbon atoms and then decreases. Comparative binding energy (COMBINE) analysis was then used to identify amino acid residues in LinB that modulate its substrate specificity. A model with three statistically significant principal components explained 95% of experimental data variability. Van der Waals interactions between substrate molecules and the enzyme dominated the COMBINE model, in agreement with the importance of substrate size in the classical QSAR model. Only a limited number of protein residues (6-8%) contribute significantly to the explanation of variability in binding affinities. The amino acid residues important for explaining variability in binding affinities are: (i) the first shell residues_Asn38, Asp108, Trp109, Glu132, Ile134, Phe143, Phe151, Phe169, Val173, Trp207, Pro208, Ile211, Leu248, and His272, (ii) the tunnel residues_Pro144, Asp147, Leu177, and Ala247, and (iii) the second shell residues_Pro39 and Phe273. The tunnel and the second shell residues represent the best targets for modulating specificity since their replacement does not lead to loss of functionality by disruption of the active site architecture. The mechanism of molecular adaptation towards different specificity is discussed based on quantitative comparison of models derived for two protein family members.

In Czech

Haloalkan dehalogenazy jsou mikrobialni enzymy, které štěpí vazbu uhlík-halogen v halogenovaných sloučeninách. dehalogenáza LinB,isolovaná z bakterie Sphingomonas paucimobilis UT26, je siroce specifický enzym.Bylo testováno 55 halogenovaných alifatických a cyklických uhlovodíků spolu s enzymem LinB. byly stanoveny konstanty Km a kcat a použita metoda QSAR ke zjištění korelace mezi kinetickými konstantami.

Links

MSM 143100005, plan (intention)

Name: Strukturně-funkční vztahy biomolekul a jejich role v metabolismu

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Structure-function Relationships and their role in the Metabolism

Citovat

KMUNÍČEK, Jan, Kamila HYNKOVÁ, Tomáš JEDLIČKA, Yuji NAGATA, Ana NEGRI, Frederico GAGO, Rebecca WADE and Jiří DAMBORSKÝ. Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26. Biochemistry. 2005, vol. 9, No 44, p. 3390-3401. ISSN 0006-2960.

@article{568607,
   author = {Kmuníček, Jan and Hynková, Kamila and Jedlička, Tomáš and Nagata, Yuji and Negri, Ana and Gago, Frederico and Wade, Rebecca and Damborský, Jiří},
   article_number = {44},
   keywords = {Haloalkane dehalogenases; Quantitative Structure-Activity Relationships (QSAR); Sphingomonas paucimobilis UT26},
   language = {eng},
   issn = {0006-2960},
   journal = {Biochemistry},
   title = {Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26},
   url = {http://loschmidt.chemi.muni.cz/peg/abstracts/biochem05a.html},
   volume = {9},
   year = {2005}
}

TY  - JOUR
ID  - 568607
AU  - Kmuníček, Jan - Hynková, Kamila - Jedlička, Tomáš - Nagata, Yuji - Negri, Ana - Gago, Frederico - Wade, Rebecca - Damborský, Jiří
PY  - 2005
TI  - Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26
JF  - Biochemistry
VL  - 9
IS  - 44
SP  - 3390-3401
EP  - 3390-3401
SN  - 00062960
KW  - Haloalkane dehalogenases
KW  - Quantitative Structure-Activity Relationships (QSAR)
KW  - Sphingomonas paucimobilis UT26
UR  - http://loschmidt.chemi.muni.cz/peg/abstracts/biochem05a.html
N2  - Haloalkane dehalogenases are microbial enzymes that cleave a carbon-halogen bond in halogenated compounds. The haloalkane dehalogenase LinB, isolated from Sphingomonas paucimobilis UT26, is a broad-specificity enzyme. Fifty five halogenated aliphatic and cyclic hydrocarbons were tested for dehalogenation with the LinB enzyme. The compounds for testing were systematically selected using a statistical experimental design. Steady-state kinetic constants Km and kcat were determined for twenty five substrates that showed detectable cleavage by the enzyme and low abiotic hydrolysis. Classical Quantitative Structure-Activity Relationships (QSAR) were used to correlate the kinetic constants with molecular descriptors and resulted in a model that explained 94% of experimental data variability. The binding affinity of the tested substrates for this haloalkane dehalogenase correlated with hydrophobicity, molecular surface, dipole moment and volume/surface ratio. Binding of the substrate molecules in the active site pocket of LinB depends non-linearly on the size of the molecules. Binding affinity increases with increasing substrate size up to a chain length of six carbon atoms and then decreases. Comparative binding energy (COMBINE) analysis was then used to identify amino acid residues in LinB that modulate its substrate specificity. A model with three statistically significant principal components explained 95% of experimental data variability. Van der Waals interactions between substrate molecules and the enzyme dominated the COMBINE model, in agreement with the importance of substrate size in the classical QSAR model. Only a limited number of protein residues (6-8%) contribute significantly to the explanation of variability in binding affinities. The amino acid residues important for explaining variability in binding affinities are: (i) the first shell residues_Asn38, Asp108, Trp109, Glu132, Ile134, Phe143, Phe151, Phe169, Val173, Trp207, Pro208, Ile211, Leu248, and His272, (ii) the tunnel residues_Pro144, Asp147, Leu177, and Ala247, and (iii) the second shell residues_Pro39 and Phe273. The tunnel and the second shell residues represent the best targets for modulating specificity since their replacement does not lead to loss of functionality by disruption of the active site architecture. The mechanism of molecular adaptation towards different specificity is discussed based on quantitative comparison of models derived for two protein family members.
ER  -

KMUNÍČEK, Jan, Kamila HYNKOVÁ, Tomáš JEDLIČKA, Yuji NAGATA, Ana NEGRI, Frederico GAGO, Rebecca WADE and Jiří DAMBORSKÝ. Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26. \textit{Biochemistry}. 2005, vol.~9, No~44, p.~3390-3401. ISSN~0006-2960.

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