Classification and evolution of P-loop GTPases and related ATPases

Leipe, Detlef D; Wolf, Yuri I; Koonin, Eugene V; Aravind, L

doi:10.1006/jmbi.2001.5378

Cited by 1,148RNA and protein synthesis mechanismsGenomics and Phylogenetic StudiesProtein Kinase Regulation and GTPase Signaling

Classification and evolution of P-loop GTPases and related ATPases

Leipe, Detlef D, Wolf, Yuri I, Koonin, Eugene V, Aravind, L·2002·Journal of Molecular Biology

DOI 10.1006/jmbi.2001.5378

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Abstract

Sequences and available structures were compared for all the widely distributed representatives of the P-loop GTPases and GTPase-related proteins with the aim of constructing an evolutionary classification for this superclass of proteins and reconstructing the principal events in their evolution. The GTPase superclass can be divided into two large classes, each of which has a unique set of sequence and structural signatures (synapomorphies). The first class, designated TRAFAC (after translation factors) includes enzymes involved in translation (initiation, elongation, and release factors), signal transduction (in particular, the extended Ras-like family), cell motility, and intracellular transport. The second class, designated SIMIBI (after signal recognition particle, MinD, and BioD), consists of signal recognition particle (SRP) GTPases, the assemblage of MinD-like ATPases, which are involved in protein localization, chromosome partitioning, and membrane transport, and a group of metabolic enzymes with kinase or related phosphate transferase activity. These two classes together contain over 20 distinct families that are further subdivided into 57 subfamilies (ancient lineages) on the basis of conserved sequence motifs, shared structural features, and domain architectures. Ten subfamilies show a universal phyletic distribution compatible with presence in the last universal common ancestor of the extant life forms (LUCA). These include four translation factors, two OBG-like GTPases, the YawG/YlqF-like GTPases (these two subfamilies also consist of predicted translation factors), the two signal-recognition-associated GTPases, and the MRP subfamily of MinD-like ATPases. The distribution of nucleotide specificity among the proteins of the GTPase superclass indicates that the common ancestor of the entire superclass was a GTPase and that a secondary switch to ATPase activity has occurred on several independent occasions during evolution. The functions of most GTPases that are traceable to LUCA are associated with translation. However, in contrast to other superclasses of P-loop NTPases (RecA-F1/F0, AAA+, helicases, ABC), GTPases do not participate in NTP-dependent nucleic acid unwinding and reorganizing activities. Hence, we hypothesize that the ancestral GTPase was an enzyme with a generic regulatory role in translation, with subsequent diversification resulting in acquisition of diverse functions in transport, protein trafficking, and signaling. In addition to the classification of previously known families of GTPases and related ATPases, we introduce several previously undetected families and describe new functional predictions.

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The Rho family is one of the 7 eukaryotic GTPase families that collectively comprise the Ras superfamily.
“The Rho family is one of the 7 eukaryotic GTPase families that collectively comprise the Ras superfamily [121,122].”
From The origins of phagocytosis and eukaryogenesis (2009) · cites this paper as [121]
The extended Ras-like family section identifies Rac/Rho as a eukaryotic subfamily, supporting Rho’s inclusion in the Ras-like grouping. The Ras-like superfamily section describes an extended family and several smaller families, but does not say that exactly seven eukaryotic GTPase families comprise it. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Bacterial small GTPases of the MglA family appeared to be the closest prokaryotic relatives of the Ras GTPases and were used to root the Ras phylogenetic tree prior to the discovery of closer prokaryotic Ras homologs.
“Bacterial small GTPases of the MglA family appeared to be the closest prokaryotic relatives of the Ras GTPases [121] and were used to root the Ras phylogenetic tree [122] prior to the recent discovery of a set of previously unknown, closer prokaryotic Ras homologs [123].”
From The origins of phagocytosis and eukaryogenesis (2009) · cites this paper as [121]
The section “The extended Ras-like family” (page unavailable) identifies bacterial MglA proteins as small prokaryotic Ras-like GTPases. It does not establish that they were the closest prokaryotic relatives of Ras GTPases. The tree-rooting and later-discovery clauses have separate citations, so they are not assessed against this source. (LLM, conf=0.82)
Experimental — accuracy not yet measured
RPPs display sequence similarity to EF-G and EF-Tu and are grouped into the translation factor superfamily of GTPases.
“The RPPs display sequence similarity to the ribosomal elongation factors, EF-G and EF-Tu (41), and are grouped into the translation factor superfamily of GTPases (27).”
From Ribosomal Protection Proteins and Their Mechanism ofTetracyclineResistance (2003) · cites this paper as [27]

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Site-directed mutagenesis of putative catalytic and nucleotide binding sites in N10-formyltetrahydrofolate synthetase
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Epigenetic Alterations in Colorectal Cancer: Emerging Biomarkers
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Comparative genomics and evolution of proteins involved in RNA metabolism
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Structural insight into filament formation by mammalian septins
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On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
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The bacterial translation stress response.
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Intersubunit Crosstalk in the Rag GTPase Heterodimer Enables mTORC1 to Respond Rapidly to Amino Acid Availability
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“This region comprises the primary “ P-loop ” domain responsible for binding phosphate during ATP synthesis/hydrolysis and is highly conserved across phosphate-binding proteins and fundamental to the activity of the ATP synthase 71,72 .”
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Authors: Leipe, D. D., Wolf, Y. I., Koonin, E. V., & Aravind, L.
Affiliations: National Institutes of Health (US)
ORCID: Wolf, Yuri I
Koonin, Eugene V
Aravind, L
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 2002-03
Volume: 317
Issue: 1
Pages: 41-72
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1006/jmbi.2001.5378
OpenAlex: W2077167882
Cited by: 1,148
References: 195
Citations by year: 2026: 26 · 2025: 38 · 2024: 45 · 2023: 40 · 2022: 45 · 2021: 58 · 2020: 57 · 2019: 57 · 2018: 52 · 2017: 39 · 2016: 42 · 2015: 49 · 2014: 56 · 2013: 63 · 2012: 43
FWCI: 14.16
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
Keywords: protein classification, translation factors, signal recognition particle, last universal common ancestor, nucleotide specificity, protein trafficking, signal transduction
MeSH terms: Adenosine Triphosphatases, Amino Acid Sequence, Animals, Multigene Family, Humans, Models, Molecular, Molecular Sequence Data, Myosins, Phylogeny, Protein Conformation, Sequence Alignment, Kinesins, Conserved Sequence, Signal Recognition Particle, Evolution, Molecular, Computational Biology, GTP Phosphohydrolases, Monomeric GTP-Binding Proteins, Heterotrimeric GTP-Binding Proteins, GTP Phosphohydrolase-Linked Elongation Factors

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Classification and evolution of P-loop GTPases and related ATPases

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