Structural stabilization of GTP-binding domains in circularly permuted GTPases: Implications for RNA binding

Anand, B.; Verma, Sunil Kumar; Prakash, Balaji

doi:10.1093/nar/gkl178

Cited by 53 publications

(69 citation statements)

References 45 publications

(77 reference statements)

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“…Interestingly, an in silico analysis of other circularly permutated GTPases (Anand et al 2006) concluded that a consequence of repositioning the G3/switch II motif within the GTPase domain is that an anchoring carboxy-terminal domain is then required to fasten switch II and maintain its efficiency for GTP binding and hydrolysis. Our finding that the carboxy-terminal zinc-finger domain is necessary for the stability of YjeQ is consistent with this model.…”

Section: Discussionmentioning

confidence: 99%

The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly

Jeganathan

Razi

Thurlow

2015

RNA

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YjeQ (also called RsgA) and RbfA proteins in Escherichia coli bind to immature 30S ribosome subunits at late stages of assembly to assist folding of the decoding center. A key step for the subunit to enter the pool of actively translating ribosomes is the release of these factors. YjeQ promotes dissociation of RbfA during the final stages of maturation; however, the mechanism implementing this functional interplay has not been elucidated. YjeQ features an amino-terminal oligonucleotide/oligosaccharide binding domain, a central GTPase module and a carboxy-terminal zinc-finger domain. We found that the zinc-finger domain is comprised of two functional motifs: the region coordinating the zinc ion and a carboxy-terminal α-helix. The first motif is essential for the anchoring of YjeQ to the 30S subunit and the carboxy-terminal α-helix facilitates the removal of RbfA once the 30S subunit reaches the mature state. Furthermore, the ability of the mature 30S subunit to stimulate YjeQ GTPase activity also depends on the carboxy-terminal α-helix. Our data are consistent with a model in which YjeQ uses this carboxy-terminal α-helix as a sensor to gauge the conformation of helix 44, an essential motif of the decoding center. According to this model, the mature conformation of helix 44 is sensed by the carboxy-terminal α-helix, which in turn stimulates the YjeQ GTPase activity. Hydrolysis of GTP is believed to assist the release of YjeQ from the mature 30S subunit through a still uncharacterized mechanism. These results identify the structural determinants in YjeQ that implement the functional interplay with RbfA.

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Section: Discussionmentioning

confidence: 99%

The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly

Jeganathan

Razi

Thurlow

2015

RNA

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“…Sequence analysis and secondary structure prediction of YqeH homologs revealed an N-terminal motif found in the treble clef family of zinc finger domains (24). The treble clef motif is contained within diverse proteins whose functions range from the binding of nucleic acids, proteins, and small molecules to the catalysis of phosphodiester bond hydrolysis (54).…”

Section: A Zinc Binding Motif In Gsyqehmentioning

confidence: 99%

“…G1-G5 are spatially close and are all associated with loop regions. G1-G4 are defined by conserved residues: G1 (GXXXXGK(S/T)), G2 (T), G3 (DXXG), G4 ((N/ T)KXD) (24,56). Interestingly, in YqeH, the G-regions of the CPG domain are rearranged as G4-G5-G1-G2-G3 in the linear sequence (Fig.…”

Section: The Crystallographic Structure Of Gsyqeh (Cpg and C-terminalmentioning

confidence: 99%

The Structure of YqeH

Sudhamsu

Lee

Klessig

et al. 2008

Journal of Biological Chemistry

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AtNOS1/AtNOA1 was identified as a nitric oxide-generating enzyme in plants, but that function has recently been questioned. To resolve issues surrounding AtNOA1 activity, we report the biochemical properties and a 2.36 Å resolution crystal structure of a bacterial AtNOA1 ortholog (YqeH). Geobacillus YqeH fused to a putative AtNOA1 leader peptide complements growth and morphological defects of Atnoa1 mutant plants. YqeH does not synthesize nitric oxide from L-arginine but rather hydrolyzes GTP. The YqeH structure reveals a circularly permuted GTPase domain and an unusual C-terminal ␤-domain. A small N-terminal domain, disordered in the structure, binds zinc. Structural homology among the C-terminal domain, the RNA-binding regulator TRAP, and the hypoxia factor pVHL define a recognition module for peptides and nucleic acids. TRAP residues important for RNA binding are conserved by the YqeH C-terminal domain, whose positioning is coupled to GTP hydrolysis. YqeH and AtNOA1 probably act as G-proteins that regulate nucleic acid recognition and not as nitric-oxide synthases.

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“…The 41 kDa protein possesses a central localized circular permuted GTPbinding domain with a G4-G1-G2-G3 motif (Leipe et al, 2002;Anand et al, 2006) and an N-terminal putative zinc finger domain with a conserved CXGCGX n CXRC motif . Interaction between the zinc finger domain and rRNA may be involved in the protein function (Anand et al, 2006). However, the C-terminus displays poor homology with proteins of known function, and is composed of nearly 20% of positively-charged amino acids, such as arginine, lysine and histidine.…”

Section: Introductionmentioning

confidence: 99%

The GTP-binding protein YqeH participates in biogenesis of the 30S ribosome subunit in Bacillus subtilis

et al. 2007

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Bacterial genome sequencing has revealed a novel family of P-loop GTPases that are often essential for growth. Accumulating evidence suggests that these proteins are involved in biogenesis of the 30S or 50S ribosomal subunits. YqeH is a member of this Obg/Era GTPase family, with its function remains to be uncovered. Here, we present results showing that YqeH is involved in the 30S subunit biogenesis in Bacillus subtilis. We observed a reduction in the 70S ribosome and accumulation of the free 50S subunit in YqeH-depleted cells. Interestingly, no free 30S subunit accumulation was evident. Consistent with the theory that YqeH is involved in 30S subunit biogenesis, a precursor of 16S rRNA and its degradation products were detected. Additionally, the reduction of free 30S subunit was not observed in Eradepleted cells. YqeH overexpression did not compensate for growth defects in mutants devoid of Era and vice versa. Moreover, in vitro GTPase analyses showed that YqeH possessed high intrinsic GTPase activity. In contrast, Era showed slow GTPase activity, which was enhanced by the 30S ribosomal subunit. Our findings strongly suggest that YqeH and Era function at distinct checkpoints during 30S subunit assembly. B. subtilis yqeH is classified as an essential gene due to the inability of the IPTG-dependent P spac -yqeH mutant to grow on LB or PAB agar plates in the absence of IPTG. However, in our experiments, the P spac -yqeH mutant grew in PAB liquid medium without IPTG supplementation, albeit at an impaired rate. This finding raises the interesting possibility that YqeH participates in assembly of the 30S ribosomal subunit as well as other cellular functions essential for growth on solid media.

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Structural stabilization of GTP-binding domains in circularly permuted GTPases: Implications for RNA binding

Cited by 53 publications

References 45 publications

The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly

The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly

The Structure of YqeH

The GTP-binding protein YqeH participates in biogenesis of the 30S ribosome subunit in Bacillus subtilis

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