Enzyme catalysis prior to aromatic residues: Reverse
engineering of a dephospho-CoA kinase

J 2021

Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase

MAKAROV, M., J. MENG, V. TRETYACHENKO, P. SRB, A. BREZINOVA et. al.

Basic information

Original name

Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase

Authors

MAKAROV, M., J. MENG, V. TRETYACHENKO, P. SRB, A. BREZINOVA, V.G. GIACOBELLI, L. BEDNAROVA, J. VONDRASEK, A.K. DUNKER and K. HLOUCHOVA

Edition

PROTEIN SCIENCE, 2021, 0961-8368

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 6.993

RIV identification code

RIV/00216224:14740/21:00124510

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1002/pro.4068

UT WoS

000632928300001

Keywords in English

aromatic amino acidscatalysis evolutiongenetic code evolutionprotein disorderprotein structure evolution

Abstract

V originále

The wide variety of protein structures and functions results from the diverse properties of the 20 canonical amino acids. The generally accepted hypothesis is that early protein evolution was associated with enrichment of a primordial alphabet, thereby enabling increased protein catalytic efficiencies and functional diversification. Aromatic amino acids were likely among the last additions to genetic code. The main objective of this study was to test whether enzyme catalysis can occur without the aromatic residues (aromatics) by studying the structure and function of dephospho-CoA kinase (DPCK) following aromatic residue depletion. We designed two variants of a putative DPCK from Aquifex aeolicus by substituting (a) Tyr, Phe and Trp or (b) all aromatics (including His). Their structural characterization indicates that substituting the aromatics does not markedly alter their secondary structures but does significantly loosen their side chain packing and increase their sizes. Both variants still possess ATPase activity, although with 150-300 times lower efficiency in comparison with the wild-type phosphotransferase activity. The transfer of the phosphate group to the dephospho-CoA substrate becomes heavily uncoupled and only the His-containing variant is still able to perform the phosphotransferase reaction. These data support the hypothesis that proteins in the early stages of life could support catalytic activities, albeit with low efficiencies. An observed significant contraction upon ligand binding is likely important for appropriate organization of the active site. Formation of firm hydrophobic cores, which enable the assembly of stably structured active sites, is suggested to provide a selective advantage for adding the aromatic residues.

Links

90127, large research infrastructures

Name: CIISB II

Citovat

MAKAROV, M., J. MENG, V. TRETYACHENKO, P. SRB, A. BREZINOVA, V.G. GIACOBELLI, L. BEDNAROVA, J. VONDRASEK, A.K. DUNKER and K. HLOUCHOVA. Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase. PROTEIN SCIENCE. 2021, vol. 30, No 5, p. 1022-1034. ISSN 0961-8368. Available from: https://dx.doi.org/10.1002/pro.4068.

@article{1846462,
   author = {Makarov, M. and Meng, J. and Tretyachenko, V. and Srb, P. and Brezinova, A. and Giacobelli, V.G. and Bednarova, L. and Vondrasek, J. and Dunker, A.K. and Hlouchova, K.},
   article_number = {5},
   doi = {http://dx.doi.org/10.1002/pro.4068},
   keywords = {aromatic amino acidscatalysis evolutiongenetic code evolutionprotein disorderprotein structure evolution},
   language = {eng},
   issn = {0961-8368},
   journal = {PROTEIN SCIENCE},
   title = {Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase},
   url = {https://onlinelibrary.wiley.com/doi/epdf/10.1002/pro.4068},
   volume = {30},
   year = {2021}
}

TY  - JOUR
ID  - 1846462
AU  - Makarov, M. - Meng, J. - Tretyachenko, V. - Srb, P. - Brezinova, A. - Giacobelli, V.G. - Bednarova, L. - Vondrasek, J. - Dunker, A.K. - Hlouchova, K.
PY  - 2021
TI  - Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase
JF  - PROTEIN SCIENCE
VL  - 30
IS  - 5
SP  - 1022-1034
EP  - 1022-1034
SN  - 09618368
KW  - aromatic amino acidscatalysis evolutiongenetic code evolutionprotein disorderprotein structure evolution
UR  - https://onlinelibrary.wiley.com/doi/epdf/10.1002/pro.4068
N2  - The wide variety of protein structures and functions results from the diverse properties of the 20 canonical amino acids. The generally accepted hypothesis is that early protein evolution was associated with enrichment of a primordial alphabet, thereby enabling increased protein catalytic efficiencies and functional diversification. Aromatic amino acids were likely among the last additions to genetic code. The main objective of this study was to test whether enzyme catalysis can occur without the aromatic residues (aromatics) by studying the structure and function of dephospho-CoA kinase (DPCK) following aromatic residue depletion. We designed two variants of a putative DPCK from Aquifex aeolicus by substituting (a) Tyr, Phe and Trp or (b) all aromatics (including His). Their structural characterization indicates that substituting the aromatics does not markedly alter their secondary structures but does significantly loosen their side chain packing and increase their sizes. Both variants still possess ATPase activity, although with 150-300 times lower efficiency in comparison with the wild-type phosphotransferase activity. The transfer of the phosphate group to the dephospho-CoA substrate becomes heavily uncoupled and only the His-containing variant is still able to perform the phosphotransferase reaction. These data support the hypothesis that proteins in the early stages of life could support catalytic activities, albeit with low efficiencies. An observed significant contraction upon ligand binding is likely important for appropriate organization of the active site. Formation of firm hydrophobic cores, which enable the assembly of stably structured active sites, is suggested to provide a selective advantage for adding the aromatic residues.
ER  -

MAKAROV, M., J. MENG, V. TRETYACHENKO, P. SRB, A. BREZINOVA, V.G. GIACOBELLI, L. BEDNAROVA, J. VONDRASEK, A.K. DUNKER and K. HLOUCHOVA. Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase. \textit{PROTEIN SCIENCE}. 2021, vol.~30, No~5, p.~1022-1034. ISSN~0961-8368. Available from: https://dx.doi.org/10.1002/pro.4068.

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