This entry represents a three-gene system broadly conserved among the Actinobacteria which includes MSMEG_4193 and homologues. Another member of the trio is a probable kinase, related to phosphatidylinositol kinases; that context supports the hypothesis that this protein acts as a phosphomutase.
This entry includes a group of RhoGEFs, including Kalirin and TRIO from mammals. Kalirin and TRIO are encoded by separate genes in mammals and by a single one in invertebrates. Kalirin and TRIO share the same complex multidomain structure and display several splice variants. They are implicated in secretory granule (SG) maturation and exocytosis [, ]. The longest Kalirin and TRIO proteins have a Sec14 domain, a stretch of spectrin repeats, a RhoGEF(DH)/PH cassette (also called GEF1), an SH3 domain, a second RhoGEF(DH)/PH cassette (also called GEF2), a second SH3 domain, Ig/FNIII domains, and a kinase domain. The first RhoGEF(DH)/PH cassette catalyzes exchange on Rac1 and RhoG while the second RhoGEF(DH)/PH cassette is specific for RhoA. Kalirin and TRIO are closely related to p63RhoGEF and have PH domains of similar function. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner [, ].Triple functional domain protein (TRIO) contains a protein kinase domain and two guanine nucleotide exchange factor (GEF) domains []. These functional domains suggest that it may play a role in signalling pathways controlling cell proliferation []. TRIO may form a complex with LAR transmembrane protein tyrosine phosphatase (PT-Pase), which localises to the ends of focal adhesions and plays an important part in coordinating cell-matrix and cytoskeletal rearrangements necessary for cell migration []. Its expression is associated with invasive tumor growth and rapid tumor cell proliferation in urinary bladder cancer [].Kalirin () promotes the exchange of GDP by GTP and stimulates the activity of specific Rho GTPases []. There are several Kalirin isoforms in humans and mice. Each Kalirin isoform is composed of a unique collection of domains and may have different functions []. In rat, isoforms 1 and 7 are necessary for neuronal development and axonal outgrowth, while isoform 6 is required for dendritic spine formation []. In humans, the major isoform of Kalirin in the adult brain is Kalirin-7, which plays a critical role in spine formation/synaptic plasticity. Kalirin-7 has been linked to neuropsychiatric and neurological diseases such as Alzheimer's, Huntingtin's, ischemic stroke, schizophrenia, depression, and cocaine addiction [, , ].
This entry represents leucine-rich repeat-containing protein 16A (LRRC16A). In humans it is also known as CARMIL1, which belongs to the CARMIL (capping protein, Arp2/3 and Myosin-I linker) family. CARMIL family members are potential regulators of actin capping proteins, which control the polymerisation of actin filaments by capping their barbed ends [, ]. CARMIL1 is essential for cell migration and may control lamellipodial actin assembly via effects on Trio and Rac1 [, ].
The CRAL-TRIO domain is a protein structural domain that binds small lipophilic molecules []. The domain is named after cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor.The CRAL-TRIO domain is found in GTPase-activating proteins (GAPs), guanine nucleotide exchange factors (GEFs) and a family of hydrophobic ligand binding proteins, including the yeast SEC14 protein and mammalian retinaldehyde- and alpha-tocopherol-binding proteins. The domain may either constitute all of the protein or only part of it [, , , ].The structure of the domain in SEC14 proteins has been determined []. The structure contains several alpha helices as well as a beta sheet composed of 6 strands. Strands 2,3,4 and 5 form a parallel beta sheet with strands 1 and 6 being anti-parallel. The structure also identified a hydrophobic binding pocket for lipid binding.
The CRAL-TRIO domain is a protein structural domain that binds small lipophilic molecules []. The domain is named after cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor.The CRAL-TRIO domain is found in GTPase-activating proteins (GAPs), guanine nucleotide exchange factors (GEFs) and a family of hydrophobic ligand binding proteins, including the yeast SEC14 protein and mammalian retinaldehyde- and alpha-tocopherol-binding proteins. The domain may either constitute all of the protein or only part of it [, , , ].The structure of the domain in SEC14 proteins has been determined []. The structure contains several alpha helices as well as a beta sheet composed of 6 strands. Strands 2,3,4 and 5 form a parallel beta sheet with strands 1 and 6 being anti-parallel. The structure also identified a hydrophobic binding pocket for lipid binding.
This narrowly distributed protein family contains an N-terminal radical SAM domain. It occurs in Pseudomonas fluorescens Pf0-1, Ralstonia solanacearum, and numerous species and strains of Burkholderia. Members always occur next to a trio of three mutually homologous genes, all of which contain the domain as the whole of the protein (about 60 amino acids) or as the C-terminal domain. The function is unknown, but the fact that all phylogenetically correlated proteins are mutually homologous with prominent invariant motifs (an invariant tyrosine and a GDL motif) and as small as 60 amino acids suggests that post-translational modification of domain-containing proteins may be its function. This view is supported by closer homology to the PqqE radical SAM protein involved in PQQ biosynthesis from the PqqA precursor peptide than to other characterised radical SAM proteins.
This entry represents the EndoU domain found at the C-terminal of EndoU endoribonucleases, which carries out a conserved RNA processing function. The EndoU domain cleaves RNA at uridylates and release 2',3'-cyclic phosphodiester ends. The EndoU domain is an α/β domain, that contains nine α-helices and three antiparallel β-sheets; the latter are clustered on one side of the domain, whereas the α-helices are largely on the other side []. It contains a conserved trio of catalytic residues, two histidines and a lysine.EndoU is a family of metal-dependent endoribonucleases that is broadly conserved among eukaryotes [, ]. EndoU family members have RNA-binding and endoribonuclease activities and appear to be involved in many aspects ofbiology, including small nucleolar RNA biogenesis, endoplasmic reticulum (ER) network formation, immune response, and neurodegeneration:Xenopus laevis endoribonuclease XendoU is responsible for processing the intron encoded U16 and U86 small nucleolar RNAs (snoRNAs) [, , ].Human EndoU, also known as PP11 (placental protein 11), has an endoribonuclease activity with placental tissue specificity [, , ].Drosophila melanogaster CG2145 and DendoU endoribonucleases [].Caenorhabditis elegans endu-2 regulates nucleotide metabolism and germ cell proliferation in response to nucleotide imbalance and other genotoxic stress [].
This entry represents a protein highly similar to the HisF protein, but generally represents the second HisF homologue in the genome where the other is an authentic HisF observed in the context of a complete histidine biosynthesis operon. The similarity between these WbuZ sequences and true HisFs is such that often the closest match by BLAST of a WbuZ is a HisF. Only by making a multiple sequence alignment is the homology relationship among the WbuZ sequences made apparent. WbuZ genes are invariably observed in the presence of a homologue of the HisH protein (designated WbuY) and a proposed N-acetyl sugar amidotransferase designated in WbuX in Escherichia coli [], IfnA in Pseudomonas aeruginosa []and PseA in Campylobacter jejuni []. Similarly, this trio of genes is invariably found in the context of saccharide biosynthesis loci. It has been shown that the WbuYZ homologues are not essential components of the activity expressed by WbuX, leading to the proposal that these to proteins provide ammonium ions to the amidotransferase when these are in low concentration []. WbuY (like HisH) is proposed to act as a glutaminase to release ammonium. In histidine biosynthesis this is also dispensable in the presence of exogenous ammonium ion. HisH and HisF form a complex such that the ammonium ion is passed directly to HisF where it is used in an amidation reaction causing a subsequent cleavage and cyclization. In the case of WbuYZ, the ammonium ion would be passed from WbuY to WbuZ. WbuZ, being non-essential and so similar to HisF that a sugar substrate is unlikely, would function instead as a ammonium channel to the WbuX protein which does the enzymatic work.
The Rho family GTPases Rho, Rac and CDC42 regulate a diverse array of cellular processes. Like all members of the Ras superfamily, the Rho proteins cycle between active GTP-bound and inactive GDP-bound conformational states.Activation of Rho proteins through release of bound GDP and subsequentbinding of GTP, is catalysed by guanine nucleotide exchange factors (GEFs) inthe Dbl family. The proteins encoded by members of the Dbl family share acommon domain, presented in this entry, of about 200 residues (designated the Dbl homology or DH domain) that has been shown to encode a GEF activity specific for a number of Rho family members. In addition, all family members possess a second, shared domain designated the pleckstrin homology (PH) domain (). Trio and its homologue UNC-73 are unique within the Dbl family insomuch as they encode two distinct DH/PH domain modules. The PH domain is invariably located immediately C-terminal to the DH domain and this invariant topography suggests a functional interdependence between these two structural modules. Biochemical data have established the role of the conserved DH domain in Rho GTPase interaction and activation, and the role of the tandem PH domain in intracellular targeting and/or regulation of DH domain function. The DH domain of Dbl has been shown to mediate oligomerisation that is mostly homophilic in nature. In addition to the tandem DH/PH domains Dbl family GEFs contain diverse structural motifs like serine/threonine kinase, RBD, PDZ, RGS, IQ, REM, Cdc25, RasGEF, CH, SH2, SH3, EF, spectrin or Ig.The DH domain is composed of three structurally conserved regions separated bymore variable regions. It does not share significant sequence homology withother subtypes of small G-protein GEF motifs such as the Cdc25 domain and theSec7 domain, which specifically interact with Ras and ARF family small GTPases, respectively, nor with other Rho protein interactive motifs, indicating that the Dbl family proteins are evolutionarily unique. The DH domain is composed of 11 alpha helices that are folded into a flattened, elongated α-helix bundle in which two of the three conserved regions, conserved region 1 (CR1) and conserved region 3 (CR3), are exposed near the centre of one surface. CR1 and CR3, together with a part of alpha-6 and the DH/PH junction site, constitute the Rho GTPase interacting pocket.
