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Protein

Small ribosomal subunit biogenesis GTPase RsgA

Gene

rsgA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

One of at least 4 proteins (Era, RbfA, RimM and RsgA/YjeQ) that assist in the late maturation steps of the functional core of the 30S ribosomal subunit (PubMed:18223068, PubMed:21102555, PubMed:21303937, PubMed:25904134, PubMed:27382067). Binds the 30S subunit contacting the head, platform, and rRNA helix 44, which may assist the last maturation stages (PubMed:21788480, PubMed:21960487). Removes RbfA from mature, but not immature 30S ribosomes in a GTP-dependent manner; 95% removal in the presence of GTP, 90% removal in GMP-PNP and 65% removal in the presence of GDP (PubMed:21102555, PubMed:25904134). Circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover (PubMed:12220175). Dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96-fold increase in kcat) ribosomes (PubMed:14973029). Mature 30S ribosomes stimulate intrinsic GTPase more than do immature 30S ribosomes (PubMed:25904134). Ribosome-associated GTPase activity is stimulated by RbfA (PubMed:21102555). The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin (PubMed:15466596) streptomycin and spectinomycin (PubMed:15828870). This inhibition is not due to competition for binding sites on the 30S or 70S ribosome (PubMed:15828870).2 Publications6 Publications

Cofactori

Zn2+UniRule annotationNote: Binds 1 zinc ion per subunit.UniRule annotation

Kineticsi

Measured in the absence of 30S ribosomes, kcat is 8.1 hour(-1) for GTP, 5.2 for dATP, 3.5 for ATP, 4.5 for ITP, 7.1 for dGTP, 2.1 for CTP.1 Publication
  1. KM=0.41 mM for GTP1 Publication
  2. KM=1.0 mM for dATP1 Publication
  3. KM=1.2 mM for ATP1 Publication
  4. KM=1.3 mM for ITP1 Publication
  5. KM=1.6 mM for dGTP1 Publication
  6. KM=2.4 mM for CTP1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi297ZincUniRule annotation1
    Metal bindingi302ZincUniRule annotation1
    Metal bindingi304Zinc; via pros nitrogenUniRule annotation1
    Metal bindingi310ZincUniRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi160 – 163GTPUniRule annotation4
    Nucleotide bindingi214 – 222GTPUniRule annotation9

    GO - Molecular functioni

    • GDP binding Source: EcoCyc
    • GTPase activity Source: EcoCyc
    • GTP binding Source: UniProtKB-KW
    • metal ion binding Source: UniProtKB-KW
    • rRNA binding Source: UniProtKB-KW

    GO - Biological processi

    • ribosomal small subunit biogenesis Source: EcoCyc

    Keywordsi

    Molecular functionHydrolase, RNA-binding, rRNA-binding
    Biological processRibosome biogenesis
    LigandGTP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:G7841-MONOMER.
    MetaCyc:G7841-MONOMER.
    SABIO-RKiP39286.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Small ribosomal subunit biogenesis GTPase RsgAUniRule annotation (EC:3.6.1.-UniRule annotation)
    Gene namesi
    Name:rsgA1 PublicationUniRule annotation
    Synonyms:engC, yjeQ
    Ordered Locus Names:b4161, JW4122
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12479. rsgA.

    Subcellular locationi

    • Cytoplasm UniRule annotation1 Publication
    • Note: Associates with 30S ribosomes (PubMed:14973029).1 Publication

    GO - Cellular componenti

    • cytosol Source: EcoCyc

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    Reduced growth rate, reduced 70S ribosomes, accumulation of 17S rRNA (the precursor of 16S rRNA) (PubMed:15466596, PubMed:21303937, PubMed:25904134, PubMed:27382067). Ribosomal proteins S2 and S21 not found in 30S subunits, decreased S3 and RbfA in 30S subunits, distortion of rRNA helix 44 near the decoding center (PubMed:21303937, PubMed:27382067). The phenotype is partially suppressed by overexpression of a number of genes involved in ribosome function, including infB, era and ksgA (PubMed:15466596). Double rbfA-rsgA deletion mutants have the same phenotype as single mutants (PubMed:21102555). Single rgsA deletion is suppressed by a number of mutants in RbfA but not by wild-type RbfA; in all the RbfA mutants less RbfA is found bound to the 30S ribosome (PubMed:21102555).5 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi1 – 20Missing : Loss of GMP-PNP-dependent association with 30S ribosomal subunit, increased association with 50S and 70S ribosomes. 1 PublicationAdd BLAST20
    Mutagenesisi220K → A: Reduction in GTPase activity, 38% of wild-type kcat for GTP. Strong reduction, 5.2% of wild-type kcat for GTP; when associated with A-221. 1 Publication1
    Mutagenesisi221S → A: Reduction in GTPase activity, 22% of wild-type kcat for GTP. GTPase activity not stimulated by 30S ribosomes (PubMed:14973029). Strong reduction, 5.2% of wild-type kcat for GTP; when associated with A-220. 2 Publications1
    Mutagenesisi250T → A: Loss of GTPase activity, does not dissociate RbfA. 1 Publication1
    Mutagenesisi298 – 300KYR → AYA: About 2-fold decreased binding to mature and immature 30S ribosomes, GTPase activity stimulated by ribosomes. 1 Publication3
    Mutagenesisi320 – 350Missing : Slightly increased specific binding to mature and immature 30S ribosomes, GTPase activity not stimulated by ribosomes. No longer removes RbfA from mature 30S ribosomes, increases RbfA-binding about 5-fold. Does not complement a deletion mutant in vivo, fewer 70S ribosomes, slower growth than deletion mutant. 1 PublicationAdd BLAST31

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000081491 – 350Small ribosomal subunit biogenesis GTPase RsgAAdd BLAST350

    Proteomic databases

    PaxDbiP39286.
    PRIDEiP39286.

    Interactioni

    Subunit structurei

    Monomer (Probable). All of the protein is associated with ribosomes; the ratio is substoichiometric at 1:200 RsgA/ribosome (PubMed:14973029). Association is tightest with the 30S subunit in the presence of the non-hydrolyzable GTP analog GMP-PNP (PubMed:14973029, PubMed:15466596). 2 cryoelectron microscopy (cryo-EM) structures in complex with 30S ribosomes have been resolved; the protein is determined to bind to different but partially overlapping regions of the 30S ribosomal subunit (PubMed:21788480, PubMed:21960487). One cryo-EM study suggests it contacts ribosomal proteins S3, S12 and S13 as well as 16S rRNA (PubMed:21788480). Another cryo-EM study shows it to bind 16S rRNA, no ribosomal proteins, and to cover the sites of intersubunit bridges B2a, B3 and B7a (PubMed:21960487). Has a significant preference for mature versus immature 30S ribosomes in the presence of GMP-PNP (PubMed:21102555, PubMed:27382067). Another study shows it binds equally well to mature and immature 30S ribosomal subunits in the presence of GMP-PNP (PubMed:25904134).1 Publication7 Publications

    Protein-protein interaction databases

    BioGridi4261080. 599 interactors.
    DIPiDIP-12581N.
    IntActiP39286. 32 interactors.
    MINTiMINT-7290812.
    STRINGi316385.ECDH10B_4356.

    Structurei

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2YKRelectron microscopy9.80W1-350[»]
    4A2Ielectron microscopy16.50V35-337[»]
    5NO2electron microscopy5.16Z34-346[»]
    5NO3electron microscopy5.16Z34-346[»]
    5NO4electron microscopy5.16Z34-346[»]
    5UZ4electron microscopy5.80Z6-339[»]
    ProteinModelPortaliP39286.
    SMRiP39286.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39286.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini104 – 273CP-type GAdd BLAST170

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni1 – 113Necessary for association with the ribosome and for stimulation of GTPase activity by 30S ribosomes1 PublicationAdd BLAST113
    Regioni1 – 20Necessary for GMP-PNP-dependent association with the 30S ribosomal subunit2 Publications1 PublicationAdd BLAST20
    Regioni287 – 319Required for binding to mature and immature 30S ribosomes1 PublicationAdd BLAST33
    Regioni320 – 350Required to remove RbfA from mature 30S ribosomes1 PublicationAdd BLAST31

    Domaini

    Has 3 domains; an N-terminal OB-like domain (about residues 1-100), a central, circularly permutated GTPase module (residues 104-270) and the C-terminal zinc-finger domain (residues 280 to 350) (PubMed:25904134). The C-terminal domain has 2 regions; the zinc-binding domain (residues 287-319) is required for binding to 30S ribosomes while the extreme C-terminus (residues 320-350) helps remove RbfA from the mature 30S subunit.1 Publication

    Sequence similaritiesi

    Belongs to the TRAFAC class YlqF/YawG GTPase family. RsgA subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105E06. Bacteria.
    COG1162. LUCA.
    HOGENOMiHOG000006957.
    InParanoidiP39286.
    KOiK06949.
    PhylomeDBiP39286.

    Family and domain databases

    CDDicd01854. YjeQ_EngC. 1 hit.
    HAMAPiMF_01820. GTPase_RsgA. 1 hit.
    InterProiView protein in InterPro
    IPR030378. G_CP_dom.
    IPR027417. P-loop_NTPase.
    IPR004881. Ribosome_biogen_GTPase_RsgA.
    IPR010914. RsgA_GTPase_dom.
    PANTHERiPTHR32120. PTHR32120. 1 hit.
    PfamiView protein in Pfam
    PF03193. RsgA_GTPase. 1 hit.
    SUPFAMiSSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00157. TIGR00157. 1 hit.
    PROSITEiView protein in PROSITE
    PS50936. ENGC_GTPASE. 1 hit.
    PS51721. G_CP. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P39286-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKNKLSKGQ QRRVNANHQR RLKTSKEKPD YDDNLFGEPD EGIVISRFGM
    60 70 80 90 100
    HADVESADGD VHRCNIRRTI RSLVTGDRVV WRPGKPAAEG VNVKGIVEAV
    110 120 130 140 150
    HERTSVLTRP DFYDGVKPIA ANIDQIVIVS AILPELSLNI IDRYLVACET
    160 170 180 190 200
    LQIEPIIVLN KIDLLDDEGM AFVNEQMDIY RNIGYRVLMV SSHTQDGLKP
    210 220 230 240 250
    LEEALTGRIS IFAGQSGVGK SSLLNALLGL QKEILTNDIS DNSGLGQHTT
    260 270 280 290 300
    TAARLYHFPH GGDVIDSPGV REFGLWHLEP EQITQGFVEF HDYLGLCKYR
    310 320 330 340 350
    DCKHDTDPGC AIREAVEEGK IAETRFENYH RILESMAQVK TRKNFSDTDD
    Length:350
    Mass (Da):39,193
    Last modified:December 15, 1998 - v2
    Checksum:iDEB14E36D2F0F378
    GO

    Sequence cautioni

    The sequence AAA97060 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Mass spectrometryi

    Molecular mass is 36830 Da from positions 21 - 350. Determined by ESI. Overexpressed protein is missing the first 20 residues.1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U14003 Genomic DNA. Translation: AAA97060.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC77121.2.
    AP009048 Genomic DNA. Translation: BAE78165.1.
    PIRiS56389.
    RefSeqiNP_418585.4. NC_000913.3.
    WP_000041964.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77121; AAC77121; b4161.
    BAE78165; BAE78165; BAE78165.
    GeneIDi948674.
    KEGGiecj:JW4122.
    eco:b4161.
    PATRICifig|1411691.4.peg.2537.

    Similar proteinsi

    Entry informationi

    Entry nameiRSGA_ECOLI
    AccessioniPrimary (citable) accession number: P39286
    Secondary accession number(s): Q2M6E1
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: December 15, 1998
    Last modified: August 30, 2017
    This is version 147 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    Was initially characterized with a propeptide of 20 residues; this is now thought to be the result of in vitro proteolysis when the protein is overexpressed (PubMed:12220175, PubMed:14973029).2 Publications

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families