Light-Emitting Dehalogenases: Reconstruction of Multifunctional
Biocatalysts

J 2019

Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts

CHALOUPKOVÁ, Radka, Veronika LIŠKOVÁ, Martin TOUL, Klára MARKOVÁ, Eva ŠEBESTOVÁ et. al.

Basic information

Original name

Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts

Authors

CHALOUPKOVÁ, Radka (203 Czech Republic, belonging to the institution), Veronika LIŠKOVÁ (203 Czech Republic, belonging to the institution), Martin TOUL (203 Czech Republic, belonging to the institution), Klára MARKOVÁ (203 Czech Republic, belonging to the institution), Eva ŠEBESTOVÁ (203 Czech Republic, belonging to the institution), Lenka HERNYCHOVÁ (203 Czech Republic), Martin MAREK (203 Czech Republic, belonging to the institution), José Gaspar RANGEL PAMPLONA PIZARRO PINTO (620 Portugal, belonging to the institution), Daniel PLUSKAL (203 Czech Republic, belonging to the institution), Jitka WATERMAN (203 Czech Republic), Zbyněk PROKOP (203 Czech Republic, guarantor, belonging to the institution) and Jiří DAMBORSKÝ (203 Czech Republic, belonging to the institution)

Edition

ACS Catalysis, Washington, D.C. AMER CHEMICAL SOC, 2019, 2155-5435

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Full Text

Impact factor

Impact factor: 12.350

RIV identification code

RIV/00216224:14310/19:00107511

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1021/acscatal.9b01031

UT WoS

000471212600009

Keywords in English

catalytic promiscuity; ancestral reconstruction; haloalkane dehalogenase; monooxygenase; luciferase; emergence of biological function

Abstract

V originále

To obtain structural insights into the emergence of biological functions from catalytically promiscuous enzymes, we reconstructed an ancestor of catalytically distinct, but evolutionarily related, haloalkane dehalogenases (EC 3.8.1.5) and Renilla luciferase (EC 1.13.12.5). This ancestor has both hydrolase and monooxygenase activities. Its crystal structure solved to 1.39 angstrom resolution revealed the presence of a catalytic pentad conserved in both dehalogenase and luciferase descendants and a molecular oxygen bound in between two residues typically stabilizing a halogen anion. The differences in the conformational dynamics of the specificity-determining cap domains between the ancestral and descendant enzymes were accessed by molecular dynamics and hydrogen-deuterium exchange mass spectrometry. Stopped-flow analysis revealed that the alkyl enzyme intermediate formed in the luciferase-catalyzed reaction is trapped by blockage of a hydrolytic reaction step. A single-point mutation (Ala54Pro) adjacent to one of the catalytic residues bestowed hydrolase activity on the modern luciferase by enabling cleavage of this intermediate. Thus, a single substitution next to the catalytic pentad may enable the emergence of promiscuous activity at the enzyme class level, and ancestral reconstruction has a clear potential for obtaining multifunctional catalysts.

Links

EF16_013/0001761, research and development project

Name: RECETOX RI

GA16-24223S, research and development project

Name: Strukturní podstata vzniku nových enzymových aktivit

Investor: Czech Science Foundation

LM2015043, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

Investor: Ministry of Education, Youth and Sports of the CR

LM2015051, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX RI)

Investor: Ministry of Education, Youth and Sports of the CR

LO1214, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

CHALOUPKOVÁ, Radka, Veronika LIŠKOVÁ, Martin TOUL, Klára MARKOVÁ, Eva ŠEBESTOVÁ, Lenka HERNYCHOVÁ, Martin MAREK, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Daniel PLUSKAL, Jitka WATERMAN, Zbyněk PROKOP and Jiří DAMBORSKÝ. Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts. ACS Catalysis. Washington, D.C.: AMER CHEMICAL SOC, 2019, vol. 9, No 6, p. 4810-4823. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.9b01031.

@article{1545949,
   author = {Chaloupková, Radka and Lišková, Veronika and Toul, Martin and Marková, Klára and Šebestová, Eva and Hernychová, Lenka and Marek, Martin and Rangel Pamplona Pizarro Pinto, José Gaspar and Pluskal, Daniel and Waterman, Jitka and Prokop, Zbyněk and Damborský, Jiří},
   article_location = {Washington, D.C.},
   article_number = {6},
   doi = {http://dx.doi.org/10.1021/acscatal.9b01031},
   keywords = {catalytic promiscuity; ancestral reconstruction; haloalkane dehalogenase; monooxygenase; luciferase; emergence of biological function},
   language = {eng},
   issn = {2155-5435},
   journal = {ACS Catalysis},
   title = {Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts},
   url = {https://pubs.acs.org/doi/abs/10.1021/acscatal.9b01031},
   volume = {9},
   year = {2019}
}

TY  - JOUR
ID  - 1545949
AU  - Chaloupková, Radka - Lišková, Veronika - Toul, Martin - Marková, Klára - Šebestová, Eva - Hernychová, Lenka - Marek, Martin - Rangel Pamplona Pizarro Pinto, José Gaspar - Pluskal, Daniel - Waterman, Jitka - Prokop, Zbyněk - Damborský, Jiří
PY  - 2019
TI  - Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts
JF  - ACS Catalysis
VL  - 9
IS  - 6
SP  - 4810-4823
EP  - 4810-4823
PB  - AMER CHEMICAL SOC
SN  - 21555435
KW  - catalytic promiscuity
KW  - ancestral reconstruction
KW  - haloalkane dehalogenase
KW  - monooxygenase
KW  - luciferase
KW  - emergence of biological function
UR  - https://pubs.acs.org/doi/abs/10.1021/acscatal.9b01031
L2  - https://pubs.acs.org/doi/abs/10.1021/acscatal.9b01031
N2  - To obtain structural insights into the emergence of biological functions from catalytically promiscuous enzymes, we reconstructed an ancestor of catalytically distinct, but evolutionarily related, haloalkane dehalogenases (EC 3.8.1.5) and Renilla luciferase (EC 1.13.12.5). This ancestor has both hydrolase and monooxygenase activities. Its crystal structure solved to 1.39 angstrom resolution revealed the presence of a catalytic pentad conserved in both dehalogenase and luciferase descendants and a molecular oxygen bound in between two residues typically stabilizing a halogen anion. The differences in the conformational dynamics of the specificity-determining cap domains between the ancestral and descendant enzymes were accessed by molecular dynamics and hydrogen-deuterium exchange mass spectrometry. Stopped-flow analysis revealed that the alkyl enzyme intermediate formed in the luciferase-catalyzed reaction is trapped by blockage of a hydrolytic reaction step. A single-point mutation (Ala54Pro) adjacent to one of the catalytic residues bestowed hydrolase activity on the modern luciferase by enabling cleavage of this intermediate. Thus, a single substitution next to the catalytic pentad may enable the emergence of promiscuous activity at the enzyme class level, and ancestral reconstruction has a clear potential for obtaining multifunctional catalysts.
ER  -

CHALOUPKOVÁ, Radka, Veronika LIŠKOVÁ, Martin TOUL, Klára MARKOVÁ, Eva ŠEBESTOVÁ, Lenka HERNYCHOVÁ, Martin MAREK, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Daniel PLUSKAL, Jitka WATERMAN, Zbyněk PROKOP and Jiří DAMBORSKÝ. Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts. \textit{ACS Catalysis}. Washington, D.C.: AMER CHEMICAL SOC, 2019, vol.~9, No~6, p.~4810-4823. ISSN~2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.9b01031.

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