Taxonomic distribution of proteins containing SRP54 domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing SRP54 domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Crystal structure of the NG domain from the signal-recognition particlereceptor FtsY.

Montoya G, Svensson C, Luirink J, Sinning I
Nature. 1997; 385: 365-8

Newly synthesized proteins destined either for secretion or incorporationinto membranes are targeted to the membrane translocation machinery by aubiquitous system consisting of a signal-recognition particle (SRP) andits receptor. Both the SRP receptor and the protein within the SRP thatbinds the signal sequence contain GTPases. These two proteins, togetherwith the RNA component of the SRP, form a complex and thereby regulateeach other's GTPase activity. Here we report the structure of theGTPase-containing portion of FtsY, the functional homologue of the SRPreceptor of Escherichia coli, at 2.2 A resolution without boundnucleotide. This so-called NG domain displays similarities to theRas-related GTPases, as well as features unique to the SRP-type GTPases,such as a separate amino-terminal domain, an insertion within the p21ras(Ras) effector domain, and a wide-open GTP-binding region. The structureexplains the low affinity of FtsY for GTP, and suggests rearrangementsthat may occur on nucleotide binding. It also identifies regionspotentially involved in the transmission of signals between domains and ininteractions with regulatory proteins.

Molecular evolution of SRP cycle components: functional implications.

Althoff S, Selinger D, Wise JA
Nucleic Acids Res. 1994; 22: 1933-47

Signal recognition particle (SRP) is a cytoplasmic ribonucleoprotein thattargets a subset of nascent presecretory proteins to the endoplasmicreticulum membrane. We have considered the SRP cycle from the perspectiveof molecular evolution, using recently determined sequences of genes orcDNAs encoding homologs of SRP (7SL) RNA, the Srp54 protein (Srp54p), andthe alpha subunit of the SRP receptor (SR alpha) from a broad spectrum oforganisms, together with the remaining five polypeptides of mammalian SRP.Our analysis provides insight into the significance of structuralvariation in SRP RNA and identifies novel conserved motifs in proteincomponents of this pathway. The lack of congruence between an establishedphylogenetic tree and size variation in 7SL homologs implies theoccurrence of several independent events that eliminated more than halfthe sequence content of this RNA during bacterial evolution. Theapparently non-essential structures are domain I, a tRNA-like element thatis constant in archaea, varies in size among eucaryotes, and is generallymissing in bacteria, and domain III, a tightly base-paired hairpin that ispresent in all eucaryotic and archeal SRP RNAs but is invariably absent inbacteria. Based on both structural and functional considerations, wepropose that the conserved core of SRP consists minimally of the 54 kDasignal sequence-binding protein complexed with the loosely base-paireddomain IV helix of SRP RNA, and is also likely to contain a homolog of theSrp68 protein. Comparative sequence analysis of the methionine-rich Mdomains from a diverse array of Srp54p homologs reveals an extended regionof amino acid identity that resembles a recently identified RNArecognition motif. Multiple sequence alignment of the G domains of Srp54pand SR alpha homologs indicates that these two polypeptides exhibitsignificant similarity even outside the four GTPase consensus motifs,including a block of nine contiguous amino acids in a location analogousto the binding site of the guanine nucleotide dissociation stimulator(GDS) for E. coli EF-Tu. The conservation of this sequence, in combinationwith the results of earlier genetic and biochemical studies of the SRPcycle, leads us to hypothesize that a component of the Srp68/72pheterodimer serves as the GDS for both Srp54p and SR alpha. Using aniterative alignment procedure, we demonstrate similarity between Srp68pand sequence motifs conserved among GDS proteins for small Ras-relatedGTPases. The conservation of SRP cycle components in organisms from allthree major branches of the phylogenetic tree suggests that this pathwayfor protein export is of ancient evolutionary origin.