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Kinateder, Thomas ; Drexler, Lukas ; Straub, Kristina ; Merkl, Rainer ; Sterner, Reinhard

Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis

Kinateder, Thomas , Drexler, Lukas, Straub, Kristina , Merkl, Rainer und Sterner, Reinhard (2022) Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis. Protein Science 32 (1), e4536.

Veröffentlichungsdatum dieses Volltextes: 10 Jan 2023 08:27
Artikel
DOI zum Zitieren dieses Dokuments: 10.5283/epub.53502


Zusammenfassung

The conservation of fold and chemistry of the enzymes associated with histidine biosynthesis suggests that this pathway evolved prior to the diversification of Bacteria, Archaea, and Eukaryotes. The only exception is the histidinol phosphate phosphatase (HolPase). So far, non-homologous HolPases that possess distinct folds and belong to three different protein superfamilies have been identified ...

The conservation of fold and chemistry of the enzymes associated with histidine biosynthesis suggests that this pathway evolved prior to the diversification of Bacteria, Archaea, and Eukaryotes. The only exception is the histidinol phosphate phosphatase (HolPase). So far, non-homologous HolPases that possess distinct folds and belong to three different protein superfamilies have been identified in various phylogenetic clades. However, their evolution has remained unknown to date. Here, we analyzed the evolutionary history of the HolPase from gamma-Proteobacteria (HisB-N). It has been argued that HisB-N and its closest homologue d-glycero-d-manno-heptose-1,7-bisphosphate 7-phosphatase (GmhB) have emerged from the same promiscuous ancestral phosphatase. GmhB variants catalyze the hydrolysis of the anomeric d-glycero-d-manno-heptose-1,7-bisphosphate (alpha HBP or beta HBP) with a strong preference for one anomer (alpha GmhB or beta GmhB). We found that HisB-N from Escherichia coli shows promiscuous activity for beta HBP but not alpha HBP, while beta GmhB from Crassaminicella sp. shows promiscuous activity for HolP. Accordingly, a combined phylogenetic tree of alpha GmhBs, beta GmhBs, and HisB-N sequences revealed that HisB-Ns form a compact subcluster derived from beta GmhBs. Ancestral sequence reconstruction and in vitro analysis revealed a promiscuous HolPase activity in the resurrected enzymes prior to functional divergence of the successors. The following increase in catalytic efficiency of the HolP turnover is reflected in the shape and electrostatics of the active site predicted by AlphaFold. An analysis of the phylogenetic tree led to a revised evolutionary model that proposes the horizontal gene transfer of a promiscuous beta GmhB from delta- to gamma-Proteobacteria where it evolved to the modern HisB-N.



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Details

DokumentenartArtikel
Titel eines Journals oder einer ZeitschriftProtein Science
Verlag:WILEY
Ort der Veröffentlichung:HOBOKEN
Band:32
Nummer des Zeitschriftenheftes oder des Kapitels:1
Seitenbereich:e4536
Datum10 Dezember 2022
InstitutionenBiologie und Vorklinische Medizin > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Reinhard Sterner
Biologie und Vorklinische Medizin > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Rainer Merkl
Identifikationsnummer
WertTyp
10.1002/pro.4536DOI
Stichwörter / KeywordsMULTIPLE SEQUENCE ALIGNMENT; ESCHERICHIA-COLI; PHOSPHATE PHOSPHATASE; HAD SUPERFAMILY; MOLECULAR EVOLUTION; MANNO-HEPTOSE; GENES; RECONSTRUCTION; SELECTION; PATHWAY; AlphaFold; ancestral sequence reconstruction; d-glycero-d-manno-heptose-1; 7-bisphosphate 7-phosphatase; enzyme; enzyme evolution; GmhB; HisB-N; histidinol phosphate phosphatase; horizontal gene transfer; promiscuity
Dewey-Dezimal-Klassifikation500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
StatusVeröffentlicht
BegutachtetJa, diese Version wurde begutachtet
An der Universität Regensburg entstandenJa
URN der UB Regensburgurn:nbn:de:bvb:355-epub-535025
Dokumenten-ID53502

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