EFP_ECOLI
ID EFP_ECOLI Reviewed; 188 AA.
AC P0A6N4; P33398; Q2M6F7;
DT 10-MAY-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Elongation factor P;
DE Short=EF-P;
GN Name=efp; OrderedLocusNames=b4147, JW4107;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-33; 71-80 AND
RP 86-117.
RX PubMed=1956781; DOI=10.1093/nar/19.22.6215;
RA Aoki H., Adams S.-L., Chung D.-G., Yaguchi M., Chuang S.-E., Ganoza M.C.;
RT "Cloning, sequencing and overexpression of the gene for prokaryotic factor
RT EF-P involved in peptide bond synthesis.";
RL Nucleic Acids Res. 19:6215-6220(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE OF 2-13.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [6]
RP CHARACTERIZATION.
RX PubMed=9195040; DOI=10.1016/s0300-9084(97)87619-5;
RA Aoki H., Adams S.-L., Turner M.A., Ganoza M.C.;
RT "Molecular characterization of the prokaryotic efp gene product involved in
RT a peptidyltransferase reaction.";
RL Biochimie 79:7-11(1997).
RN [7]
RP DISRUPTION PHENOTYPE.
RX PubMed=9405429; DOI=10.1074/jbc.272.51.32254;
RA Aoki H., Dekany K., Adams S.L., Ganoza M.C.;
RT "The gene encoding the elongation factor P protein is essential for
RT viability and is required for protein synthesis.";
RL J. Biol. Chem. 272:32254-32259(1997).
RN [8]
RP COPY NUMBER.
RX PubMed=7011506; DOI=10.1139/o80-177;
RA An G., Glick B.R., Friesen J.D., Ganoza M.C.;
RT "Identification and quantitation of elongation factor EF-P in Escherichia
RT coli cell-free extracts.";
RL Can. J. Biochem. 58:1312-1314(1980).
RN [9]
RP PTM, AND RIBOSOME-BINDING.
RX PubMed=18201202; DOI=10.1111/j.1742-4658.2007.06228.x;
RA Aoki H., Xu J., Emili A., Chosay J.G., Golshani A., Ganoza M.C.;
RT "Interactions of elongation factor EF-P with the Escherichia coli
RT ribosome.";
RL FEBS J. 275:671-681(2008).
RN [10]
RP BETA-LYSYLATION AT LYS-34 BY EPMA, AND HYDROXYLATION AT LYS-34.
RC STRAIN=K12;
RX PubMed=21841797; DOI=10.1038/nchembio.632;
RA Roy H., Zou S.B., Bullwinkle T.J., Wolfe B.S., Gilreath M.S., Forsyth C.J.,
RA Navarre W.W., Ibba M.;
RT "The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-
RT beta-lysine.";
RL Nat. Chem. Biol. 7:667-669(2011).
RN [11]
RP BETA-LYSYLATION AT LYS-34 BY EPMA AND EPMB, HYDROXYLATION AT LYS-34, AND
RP MUTAGENESIS OF LYS-34.
RC STRAIN=K12 / MG1655 / ATCC 47076, and MRE-600;
RX PubMed=22128152; DOI=10.1074/jbc.m111.309633;
RA Park J.H., Johansson H.E., Aoki H., Huang B.X., Kim H.Y., Ganoza M.C.,
RA Park M.H.;
RT "Post-translational modification by beta-lysylation is required for
RT activity of Escherichia coli elongation factor P (EF-P).";
RL J. Biol. Chem. 287:2579-2590(2012).
RN [12]
RP HYDROXYLATION AT LYS-34 BY EPMC, AND MASS SPECTROMETRY.
RC STRAIN=K12 / AT713, K12 / BW25113, K12 / MC4100 / ATCC 35695 / DSM 6574,
RC and MRE-600;
RX PubMed=22706199; DOI=10.1038/nchembio.1001;
RA Peil L., Starosta A.L., Virumae K., Atkinson G.C., Tenson T., Remme J.,
RA Wilson D.N.;
RT "Lys34 of translation elongation factor EF-P is hydroxylated by YfcM.";
RL Nat. Chem. Biol. 8:695-697(2012).
RN [13]
RP FUNCTION IN POLY-PRO TRANSLATION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
RP LYS-34.
RC STRAIN=K12 / BW25113, and K12 / MG1655 / ATCC 47076;
RX PubMed=23239623; DOI=10.1126/science.1228985;
RA Ude S., Lassak J., Starosta A.L., Kraxenberger T., Wilson D.N., Jung K.;
RT "Translation elongation factor EF-P alleviates ribosome stalling at
RT polyproline stretches.";
RL Science 339:82-85(2013).
RN [14]
RP FUNCTION IN TRANSLATION, AND PTM.
RC STRAIN=B / BL21-DE3, and MRE-600;
RX PubMed=23239624; DOI=10.1126/science.1229017;
RA Doerfel L.K., Wohlgemuth I., Kothe C., Peske F., Urlaub H., Rodnina M.V.;
RT "EF-P is essential for rapid synthesis of proteins containing consecutive
RT proline residues.";
RL Science 339:85-88(2013).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH LYSYL-ADENYLATE
RP ANALOG AND EMPA, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF LYS-31; GLY-33
RP AND LYS-34.
RC STRAIN=K12 / BW25113, and K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=20729861; DOI=10.1038/nsmb.1889;
RA Yanagisawa T., Sumida T., Ishii R., Takemoto C., Yokoyama S.;
RT "A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine
RT residue in translation elongation factor P.";
RL Nat. Struct. Mol. Biol. 17:1136-1143(2010).
CC -!- FUNCTION: Involved in peptide bond synthesis. Alleviates ribosome
CC stalling that occurs when 3 or more consecutive Pro residues or the
CC sequence PPG is present in a protein, possibly by augmenting the
CC peptidyl transferase activity of the ribosome. Beta-lysylation at Lys-
CC 34 is required for alleviation. The Pro codons and their context do not
CC affect activity; only consecutive Pro residues (not another amino acid)
CC are affected by EF-P. Has stimulatory effects on peptide bond formation
CC between ribosome-bound initiator tRNA(fMet) and puromycin, and N-
CC acetyl-Phe tRNA(Phe)-primed poly(U)-directed poly(Phe) synthesis.
CC {ECO:0000269|PubMed:23239623, ECO:0000269|PubMed:23239624}.
CC -!- PATHWAY: Protein biosynthesis; polypeptide chain elongation.
CC -!- SUBUNIT: Binds 30S, 50S and 70S ribosomes, possibly near the A site,
CC note that T.thermophilus structures show binding between the P and E
CC sites (PDB 3HUW and 3HUY). Proportionally less EF-P binds to larger
CC polysomes, suggesting it has a role early in translation. It is present
CC in 1 copy per 10 ribosomes. {ECO:0000269|PubMed:20729861}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- PTM: Is beta-lysylated on the epsilon-amino group of Lys-34 by the
CC combined action of EpmA and EpmB, and then hydroxylated on the C5
CC position of the same residue by EpmC. Lysylation is critical for the
CC stimulatory effect of EF-P on peptide-bond formation. The lysylation
CC moiety would extend toward the peptidyltransferase center and stabilize
CC the terminal 3-CCA end of the tRNA. The hydroxylation of the C5
CC position on Lys-34 would allow additional potential stabilizing
CC hydrogen-bond interactions with the P-tRNA (PubMed:21841797
CC PubMed:22128152 PubMed:22706199 and PubMed:20729861).
CC {ECO:0000269|PubMed:21841797, ECO:0000269|PubMed:22128152,
CC ECO:0000269|PubMed:22706199}.
CC -!- MASS SPECTROMETRY: Mass=20591.6; Method=Electrospray; Note=With N6-
CC (3,6-diaminohexanoyl)-5-hydroxy-Lys-34.;
CC Evidence={ECO:0000269|PubMed:22706199};
CC -!- DISRUPTION PHENOTYPE: Disruption of this gene leads to lethality
CC (PubMed:9405429) or to a very slow growth phenotype (PubMed:20729861).
CC Required for the expression of poly-Pro-containing proteins.
CC {ECO:0000269|PubMed:20729861, ECO:0000269|PubMed:23239623,
CC ECO:0000269|PubMed:9405429}.
CC -!- SIMILARITY: Belongs to the elongation factor P family. {ECO:0000305}.
CC -!- CAUTION: The modification on Lys-34 was initially thought to be a
CC spermidine residue. {ECO:0000305|PubMed:18201202}.
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DR EMBL; X61676; CAA43851.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97046.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77107.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78149.1; -; Genomic_DNA.
DR PIR; S34443; S34443.
DR RefSeq; NP_418571.1; NC_000913.3.
DR RefSeq; WP_000257278.1; NZ_STEB01000014.1.
DR PDB; 3A5Z; X-ray; 2.50 A; B/D/F/H=1-188.
DR PDB; 6ENJ; EM; 3.70 A; w=1-188.
DR PDB; 6ENU; EM; 3.10 A; w=1-188.
DR PDBsum; 3A5Z; -.
DR PDBsum; 6ENJ; -.
DR PDBsum; 6ENU; -.
DR AlphaFoldDB; P0A6N4; -.
DR SMR; P0A6N4; -.
DR BioGRID; 4260776; 791.
DR DIP; DIP-31834N; -.
DR IntAct; P0A6N4; 51.
DR STRING; 511145.b4147; -.
DR jPOST; P0A6N4; -.
DR PaxDb; P0A6N4; -.
DR PRIDE; P0A6N4; -.
DR EnsemblBacteria; AAC77107; AAC77107; b4147.
DR EnsemblBacteria; BAE78149; BAE78149; BAE78149.
DR GeneID; 67414765; -.
DR GeneID; 948661; -.
DR KEGG; ecj:JW4107; -.
DR KEGG; eco:b4147; -.
DR PATRIC; fig|1411691.4.peg.2553; -.
DR EchoBASE; EB2023; -.
DR eggNOG; COG0231; Bacteria.
DR HOGENOM; CLU_074944_0_0_6; -.
DR InParanoid; P0A6N4; -.
DR OMA; WSVVEFQ; -.
DR PhylomeDB; P0A6N4; -.
DR BioCyc; EcoCyc:EG12099-MON; -.
DR BioCyc; MetaCyc:EG12099-MON; -.
DR UniPathway; UPA00345; -.
DR PRO; PR:P0A6N4; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoCyc.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0043022; F:ribosome binding; IDA:EcoCyc.
DR GO; GO:0003746; F:translation elongation factor activity; IDA:EcoCyc.
DR GO; GO:2001125; P:negative regulation of translational frameshifting; IMP:EcoCyc.
DR GO; GO:0072344; P:rescue of stalled ribosome; IMP:EcoCyc.
DR GO; GO:0006414; P:translational elongation; IDA:EcoCyc.
DR CDD; cd04470; S1_EF-P_repeat_1; 1.
DR CDD; cd05794; S1_EF-P_repeat_2; 1.
DR Gene3D; 2.30.30.30; -; 1.
DR Gene3D; 2.40.50.140; -; 2.
DR HAMAP; MF_00141; EF_P; 1.
DR InterPro; IPR015365; Elong-fact-P_C.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR014722; Rib_L2_dom2.
DR InterPro; IPR020599; Transl_elong_fac_P/YeiP.
DR InterPro; IPR013185; Transl_elong_KOW-like.
DR InterPro; IPR001059; Transl_elong_P/YeiP_cen.
DR InterPro; IPR013852; Transl_elong_P/YeiP_CS.
DR InterPro; IPR011768; Transl_elongation_fac_P.
DR InterPro; IPR008991; Translation_prot_SH3-like_sf.
DR PANTHER; PTHR30053; PTHR30053; 1.
DR Pfam; PF01132; EFP; 1.
DR Pfam; PF08207; EFP_N; 1.
DR Pfam; PF09285; Elong-fact-P_C; 1.
DR PIRSF; PIRSF005901; EF-P; 1.
DR SMART; SM01185; EFP; 1.
DR SMART; SM00841; Elong-fact-P_C; 1.
DR SUPFAM; SSF50104; SSF50104; 1.
DR SUPFAM; SSF50249; SSF50249; 2.
DR TIGRFAMs; TIGR00038; efp; 1.
DR PROSITE; PS01275; EFP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Elongation factor;
KW Hydroxylation; Protein biosynthesis; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:1956781,
FT ECO:0000269|PubMed:9298646"
FT CHAIN 2..188
FT /note="Elongation factor P"
FT /id="PRO_0000094245"
FT MOD_RES 34
FT /note="N6-(3,6-diaminohexanoyl)-5-hydroxylysine"
FT /evidence="ECO:0000269|PubMed:21841797,
FT ECO:0000269|PubMed:22128152, ECO:0000269|PubMed:22706199"
FT MUTAGEN 31
FT /note="K->A: No lysylation."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 33
FT /note="G->K: No lysylation. Loss of in vivo EF-P function
FT for cell growth."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 34
FT /note="K->A: No lysylation and loss of EF-P activity. No
FT facilitation of translation of poly-Pro stretches."
FT /evidence="ECO:0000269|PubMed:20729861,
FT ECO:0000269|PubMed:22128152, ECO:0000269|PubMed:23239623"
FT STRAND 4..6
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 14..17
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 20..30
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 38..45
FT /evidence="ECO:0007829|PDB:3A5Z"
FT HELIX 46..48
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 51..57
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 73..77
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:3A5Z"
FT TURN 87..89
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 92..95
FT /evidence="ECO:0007829|PDB:3A5Z"
FT HELIX 97..100
FT /evidence="ECO:0007829|PDB:3A5Z"
FT TURN 102..106
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 109..112
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 114..118
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 152..156
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 161..164
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 173..177
FT /evidence="ECO:0007829|PDB:3A5Z"
FT TURN 178..181
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 182..186
FT /evidence="ECO:0007829|PDB:3A5Z"
SQ SEQUENCE 188 AA; 20591 MW; E36E136D4399460F CRC64;
MATYYSNDFR AGLKIMLDGE PYAVEASEFV KPGKGQAFAR VKLRRLLTGT RVEKTFKSTD
SAEGADVVDM NLTYLYNDGE FWHFMNNETF EQLSADAKAI GDNAKWLLDQ AECIVTLWNG
QPISVTPPNF VELEIVDTDP GLKGDTAGTG GKPATLSTGA VVKVPLFVQI GEVIKVDTRS
GEYVSRVK
