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.

Základní údaje

Originální název

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

Autoři

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

Vydání

PROTEIN SCIENCE, 2021, 0961-8368

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 6.993

Kód RIV

RIV/00216224:14740/21:00124510

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000632928300001

Klíčová slova anglicky

aromatic amino acidscatalysis evolutiongenetic code evolutionprotein disorderprotein structure evolution

Štítky

ne MU, rivok

Příznaky

Recenzováno

Změněno: 18. 5. 2022 15:03, Mgr. Pavla Foltynová, Ph.D.

Anotace

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.

Návaznosti

90127, velká výzkumná infrastruktura

Název: CIISB II

Citovat

MAKAROV, M., J. MENG, V. TRETYACHENKO, P. SRB, A. BREZINOVA, V.G. GIACOBELLI, L. BEDNAROVA, J. VONDRASEK, A.K. DUNKER a K. HLOUCHOVA. Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase. PROTEIN SCIENCE. 2021, roč. 30, č. 5, s. 1022-1034. ISSN 0961-8368. Dostupné z: 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 a K. HLOUCHOVA. Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase. \textit{PROTEIN SCIENCE}. 2021, roč.~30, č.~5, s.~1022-1034. ISSN~0961-8368. Dostupné z: https://dx.doi.org/10.1002/pro.4068.

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