SPEFL_ECOLI
ID SPEFL_ECOLI Reviewed; 34 AA.
AC P0DTV7;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 17-JUN-2020, sequence version 1.
DT 03-AUG-2022, entry version 8.
DE RecName: Full=Leader peptide SpeFL {ECO:0000255|HAMAP-Rule:MF_00851, ECO:0000303|PubMed:32094585};
DE AltName: Full=Arrest peptide SpeFL {ECO:0000255|HAMAP-Rule:MF_00851, ECO:0000303|PubMed:32094585};
GN Name=speFL {ECO:0000255|HAMAP-Rule:MF_00851, ECO:0000303|PubMed:32094585};
GN OrderedLocusNames=b4803;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP STRUCTURE BY ELECTRON MICROSCOPY (2.7 ANGSTROMS) IN COMPLEX WITH STALLED
RP 70S RIBOSOMES AND ORNITHINE, FUNCTION, SUBUNIT, DOMAIN, INDUCTION, AND
RP MUTAGENESIS OF 1-MET--THR-7; 2-GLU--ARG-34; HIS-10; ILE-11; 12-ARG-ARG-13;
RP HIS-16; PHE-26; PHE-28; PHE-30 AND PHE-31.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=32094585; DOI=10.1038/s41564-020-0669-1;
RA Herrero Del Valle A., Seip B., Cervera-Marzal I., Sacheau G.,
RA Seefeldt A.C., Innis C.A.;
RT "Ornithine capture by a translating ribosome controls bacterial polyamine
RT synthesis.";
RL Nat. Microbiol. 5:554-561(2020).
CC -!- FUNCTION: A small protein (arrest peptide) encoded upstream of
CC inducible ornithine carboxylase gene (speF) that controls expression of
CC downstream genes (speF and patE) by nascent chain-translational arrest
CC and transcriptional attenuation. In the presence of ornithine a
CC toeprint due to ribosomal arrest can be seen on the speFL transcript.
CC Only L-ornithine (not other tested amino acids) has this effect
CC (PubMed:32094585). It is thought that in the presence of ornithine,
CC ribosomal stalling on speFL prevents binding of Rho transcription
CC termination factor to a downstream rut site allowing transcription of
CC the operon. In the absence of ornithine, ribosomes terminate
CC translation and are recycled, exposing the rut site allowing Rho to
CC bind and prematurely terminate transcription. The presence of a pair of
CC rare Arg codons could slow down translation to prevent polysome
CC accumulation and to expose the rut site to Rho (Probable).
CC {ECO:0000255|HAMAP-Rule:MF_00851, ECO:0000269|PubMed:32094585,
CC ECO:0000305|PubMed:32094585}.
CC -!- SUBUNIT: Binds ornithine in stalled 70S ribosomes, blocking the upper
CC two-thirds of the exit tunnel. Contacts 23S rRNA and ribosomal proteins
CC L4 and L22. {ECO:0000255|HAMAP-Rule:MF_00851,
CC ECO:0000269|PubMed:32094585}.
CC -!- INDUCTION: Induced by ornithine; putrescine does not trigger ribosome
CC stalling and so appears to repress expression. Part of the speFL-speF-
CC potE operon. {ECO:0000255|HAMAP-Rule:MF_00851,
CC ECO:0000269|PubMed:32094585}.
CC -!- DOMAIN: An N-terminal sensor domain binds ornithine already present in
CC the ribosomal exit tunnel; upon ornithine binding the downstream
CC effector domain compacts in the exit tunnel, causing a shift of 23S
CC rRNA U2585 which blocks the action of peptide chain release factor 1
CC (prfA), causing ribosome stalling. {ECO:0000305|PubMed:32094585}.
CC -!- MISCELLANEOUS: Changing the amino acid sequence by 2 frameshifts with
CC minimal nucleotide changes indicates the peptide sequence, but not mRNA
CC structure is important. {ECO:0000269|PubMed:32094585}.
CC -!- SIMILARITY: Belongs to the speF operon leader peptide family.
CC {ECO:0000255|HAMAP-Rule:MF_00851, ECO:0000305}.
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DR EMBL; U00096; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PDB; 6TBV; EM; 2.70 A; SPE1=1-34.
DR PDB; 6TC3; EM; 2.70 A; SPE1=1-34.
DR PDB; 6TVB; EM; 2.70 A; SPE1=1-34.
DR PDBsum; 6TBV; -.
DR PDBsum; 6TC3; -.
DR PDBsum; 6TVB; -.
DR AlphaFoldDB; P0DTV7; -.
DR SMR; P0DTV7; -.
DR BioCyc; EcoCyc:MON0-4532; -.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006448; P:regulation of translational elongation; IMP:EcoCyc.
DR GO; GO:0031556; P:transcriptional attenuation by ribosome; IMP:EcoCyc.
DR HAMAP; MF_00851; Leader_SpeFL; 1.
DR InterPro; IPR021237; SpeFL.
PE 1: Evidence at protein level;
KW 3D-structure; Leader peptide; Reference proteome; RNA-binding;
KW rRNA-binding; Transcription; Transcription regulation;
KW Translation regulation.
FT CHAIN 1..34
FT /note="Leader peptide SpeFL"
FT /id="PRO_0000450346"
FT REGION 1..13
FT /note="Sensor domain"
FT /evidence="ECO:0000305|PubMed:32094585"
FT REGION 14..34
FT /note="Effector domain"
FT /evidence="ECO:0000305|PubMed:32094585"
FT MOTIF 10..16
FT /note="Ornithine recognition loop"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00851,
FT ECO:0000269|PubMed:32094585"
FT BINDING 13
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00851,
FT ECO:0000269|PubMed:32094585, ECO:0007744|PDB:6TC3,
FT ECO:0007744|PDB:6TVB"
FT MUTAGEN 1..7
FT /note="Missing: Loss of ornithine-dependent translation
FT arrest in vitro."
FT /evidence="ECO:0000269|PubMed:32094585"
FT MUTAGEN 2..34
FT /note="ENNSRTMPHIRRTTHIMKFAHRNSFDFHFFNAR->KITAALCPISGGQLILS
FT SLLIAIASTFTSSMPV: Loss of ribosome stalling, nucleotide
FT sequence is almost identical."
FT /evidence="ECO:0000269|PubMed:32094585"
FT MUTAGEN 10
FT /note="H->A: Loss of ornithine-dependent translation arrest
FT in vitro."
FT /evidence="ECO:0000269|PubMed:32094585"
FT MUTAGEN 11
FT /note="I->A: Loss of ornithine-dependent translation arrest
FT in vitro."
FT /evidence="ECO:0000269|PubMed:32094585"
FT MUTAGEN 12..13
FT /note="RR->AA,KK: Loss of ornithine-dependent translation
FT arrest in vitro."
FT /evidence="ECO:0000269|PubMed:32094585"
FT MUTAGEN 16
FT /note="H->A: Loss of ornithine-dependent translation arrest
FT in vitro."
FT /evidence="ECO:0000269|PubMed:32094585"
FT MUTAGEN 26
FT /note="F->A: Loss of ornithine-dependent translation arrest
FT in vitro."
FT /evidence="ECO:0000269|PubMed:32094585"
FT MUTAGEN 28
FT /note="F->A: Loss of ornithine-dependent translation arrest
FT in vitro."
FT /evidence="ECO:0000269|PubMed:32094585"
FT MUTAGEN 30
FT /note="F->A: Loss of ornithine-dependent translation arrest
FT in vitro."
FT /evidence="ECO:0000269|PubMed:32094585"
FT MUTAGEN 31
FT /note="F->A: Loss of ornithine-dependent translation arrest
FT in vitro."
FT /evidence="ECO:0000269|PubMed:32094585"
SQ SEQUENCE 34 AA; 4249 MW; 67E222CF9D30C2C5 CRC64;
MENNSRTMPH IRRTTHIMKF AHRNSFDFHF FNAR
