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Elongation factor P (EF-P)

 EFP_ECOLI               Reviewed;         188 AA.
P0A6N4; P33398; Q2M6F7;
10-MAY-2005, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 2.
25-APR-2018, entry version 111.
RecName: Full=Elongation factor P;
Short=EF-P;
Name=efp; OrderedLocusNames=b4147, JW4107;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-33; 71-80
AND 86-117.
PubMed=1956781; DOI=10.1093/nar/19.22.6215;
Aoki H., Adams S.-L., Chung D.-G., Yaguchi M., Chuang S.-E.,
Ganoza M.C.;
"Cloning, sequencing and overexpression of the gene for prokaryotic
factor EF-P involved in peptide bond synthesis.";
Nucleic Acids Res. 19:6215-6220(1991).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=7610040; DOI=10.1093/nar/23.12.2105;
Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.,
Blattner F.R.;
"Analysis of the Escherichia coli genome VI: DNA sequence of the
region from 92.8 through 100 minutes.";
Nucleic Acids Res. 23:2105-2119(1995).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
PROTEIN SEQUENCE OF 2-13.
STRAIN=K12 / EMG2;
PubMed=9298646; DOI=10.1002/elps.1150180807;
Link A.J., Robison K., Church G.M.;
"Comparing the predicted and observed properties of proteins encoded
in the genome of Escherichia coli K-12.";
Electrophoresis 18:1259-1313(1997).
[6]
CHARACTERIZATION.
PubMed=9195040; DOI=10.1016/S0300-9084(97)87619-5;
Aoki H., Adams S.-L., Turner M.A., Ganoza M.C.;
"Molecular characterization of the prokaryotic efp gene product
involved in a peptidyltransferase reaction.";
Biochimie 79:7-11(1997).
[7]
DISRUPTION PHENOTYPE.
PubMed=9405429; DOI=10.1074/jbc.272.51.32254;
Aoki H., Dekany K., Adams S.L., Ganoza M.C.;
"The gene encoding the elongation factor P protein is essential for
viability and is required for protein synthesis.";
J. Biol. Chem. 272:32254-32259(1997).
[8]
COPY NUMBER.
PubMed=7011506;
An G., Glick B.R., Friesen J.D., Ganoza M.C.;
"Identification and quantitation of elongation factor EF-P in
Escherichia coli cell-free extracts.";
Can. J. Biochem. 58:1312-1314(1980).
[9]
PTM, AND RIBOSOME-BINDING.
PubMed=18201202; DOI=10.1111/j.1742-4658.2007.06228.x;
Aoki H., Xu J., Emili A., Chosay J.G., Golshani A., Ganoza M.C.;
"Interactions of elongation factor EF-P with the Escherichia coli
ribosome.";
FEBS J. 275:671-681(2008).
[10]
BETA-LYSYLATION AT LYS-34 BY EPMA, AND HYDROXYLATION AT LYS-34.
STRAIN=K12;
PubMed=21841797; DOI=10.1038/nchembio.632;
Roy H., Zou S.B., Bullwinkle T.J., Wolfe B.S., Gilreath M.S.,
Forsyth C.J., Navarre W.W., Ibba M.;
"The tRNA synthetase paralog PoxA modifies elongation factor-P with
(R)-beta-lysine.";
Nat. Chem. Biol. 7:667-669(2011).
[11]
BETA-LYSYLATION AT LYS-34 BY EPMA AND EPMB, HYDROXYLATION AT LYS-34,
AND MUTAGENESIS OF LYS-34.
STRAIN=K12 / MG1655 / ATCC 47076, and MRE-600;
PubMed=22128152; DOI=10.1074/jbc.M111.309633;
Park J.H., Johansson H.E., Aoki H., Huang B.X., Kim H.Y., Ganoza M.C.,
Park M.H.;
"Post-translational modification by beta-lysylation is required for
activity of Escherichia coli elongation factor P (EF-P).";
J. Biol. Chem. 287:2579-2590(2012).
[12]
HYDROXYLATION AT LYS-34 BY EPMC, AND MASS SPECTROMETRY.
STRAIN=K12 / AT713, K12 / BW25113,
K12 / MC4100 / ATCC 35695 / DSM 6574, and MRE-600;
PubMed=22706199; DOI=10.1038/nchembio.1001;
Peil L., Starosta A.L., Virumae K., Atkinson G.C., Tenson T.,
Remme J., Wilson D.N.;
"Lys34 of translation elongation factor EF-P is hydroxylated by
YfcM.";
Nat. Chem. Biol. 8:695-697(2012).
[13]
FUNCTION IN POLY-PRO TRANSLATION, DISRUPTION PHENOTYPE, AND
MUTAGENESIS OF LYS-34.
STRAIN=K12 / BW25113, and K12 / MG1655 / ATCC 47076;
PubMed=23239623; DOI=10.1126/science.1228985;
Ude S., Lassak J., Starosta A.L., Kraxenberger T., Wilson D.N.,
Jung K.;
"Translation elongation factor EF-P alleviates ribosome stalling at
polyproline stretches.";
Science 339:82-85(2013).
[14]
FUNCTION IN TRANSLATION, AND PTM.
STRAIN=B / BL21-DE3, and MRE-600;
PubMed=23239624; DOI=10.1126/science.1229017;
Doerfel L.K., Wohlgemuth I., Kothe C., Peske F., Urlaub H.,
Rodnina M.V.;
"EF-P is essential for rapid synthesis of proteins containing
consecutive proline residues.";
Science 339:85-88(2013).
[15]
X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH LYSYL-ADENYLATE
ANALOG AND EMPA, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF LYS-31;
GLY-33 AND LYS-34.
STRAIN=K12 / BW25113, and K12 / MC4100 / ATCC 35695 / DSM 6574;
PubMed=20729861; DOI=10.1038/nsmb.1889;
Yanagisawa T., Sumida T., Ishii R., Takemoto C., Yokoyama S.;
"A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine
residue in translation elongation factor P.";
Nat. Struct. Mol. Biol. 17:1136-1143(2010).
-!- FUNCTION: Involved in peptide bond synthesis. Alleviates ribosome
stalling that occurs when 3 or more consecutive Pro residues or
the sequence PPG is present in a protein, possibly by augmenting
the peptidyl transferase activity of the ribosome. Beta-lysylation
at Lys-34 is required for alleviation. The Pro codons and their
context do not affect activity; only consecutive Pro residues (not
another amino acid) are affected by EF-P. Has stimulatory effects
on peptide bond formation between ribosome-bound initiator
tRNA(fMet) and puromycin, and N-acetyl-Phe tRNA(Phe)-primed
poly(U)-directed poly(Phe) synthesis.
{ECO:0000269|PubMed:23239623, ECO:0000269|PubMed:23239624}.
-!- PATHWAY: Protein biosynthesis; polypeptide chain elongation.
-!- SUBUNIT: Binds 30S, 50S and 70S ribosomes, possibly near the A
site, note that T.thermophilus structures show binding between the
P and E sites (PDB 3HUW and 3HUY). Proportionally less EF-P binds
to larger polysomes, suggesting it has a role early in
translation. It is present in 1 copy per 10 ribosomes.
{ECO:0000269|PubMed:20729861}.
-!- SUBCELLULAR LOCATION: Cytoplasm.
-!- PTM: Is beta-lysylated on the epsilon-amino group of Lys-34 by the
combined action of EpmA and EpmB, and then hydroxylated on the C5
position of the same residue by EpmC. Lysylation is critical for
the stimulatory effect of EF-P on peptide-bond formation. The
lysylation moiety would extend toward the peptidyltransferase
center and stabilize the terminal 3-CCA end of the tRNA. The
hydroxylation of the C5 position on Lys-34 would allow additional
potential stabilizing hydrogen-bond interactions with the P-tRNA
(PubMed:21841797 PubMed:22128152 PubMed:22706199 and
PubMed:20729861). {ECO:0000269|PubMed:21841797,
ECO:0000269|PubMed:22128152, ECO:0000269|PubMed:22706199}.
-!- MASS SPECTROMETRY: Mass=20591.6; Method=Electrospray; Range=2-188;
Note=With N6-(3,6-diaminohexanoyl)-5-hydroxy-Lys-34.;
Evidence={ECO:0000269|PubMed:22706199};
-!- DISRUPTION PHENOTYPE: Disruption of this gene leads to lethality
(PubMed:9405429) or to a very slow growth phenotype
(PubMed:20729861). Required for the expression of poly-Pro-
containing proteins. {ECO:0000269|PubMed:20729861,
ECO:0000269|PubMed:23239623, ECO:0000269|PubMed:9405429}.
-!- SIMILARITY: Belongs to the elongation factor P family.
{ECO:0000305}.
-!- CAUTION: The modification on Lys-34 was initially thought to be a
spermidine residue. {ECO:0000305|PubMed:18201202}.
-----------------------------------------------------------------------
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EMBL; X61676; CAA43851.1; -; Genomic_DNA.
EMBL; U14003; AAA97046.1; -; Genomic_DNA.
EMBL; U00096; AAC77107.1; -; Genomic_DNA.
EMBL; AP009048; BAE78149.1; -; Genomic_DNA.
PIR; S34443; S34443.
RefSeq; NP_418571.1; NC_000913.3.
RefSeq; WP_000257278.1; NZ_LN832404.1.
PDB; 3A5Z; X-ray; 2.50 A; B/D/F/H=1-188.
PDB; 6ENJ; EM; 3.70 A; w=1-188.
PDB; 6ENU; EM; 3.10 A; w=1-188.
PDBsum; 3A5Z; -.
PDBsum; 6ENJ; -.
PDBsum; 6ENU; -.
ProteinModelPortal; P0A6N4; -.
SMR; P0A6N4; -.
BioGrid; 4260776; 791.
DIP; DIP-31834N; -.
IntAct; P0A6N4; 1.
STRING; 316385.ECDH10B_4340; -.
EPD; P0A6N4; -.
PaxDb; P0A6N4; -.
PRIDE; P0A6N4; -.
EnsemblBacteria; AAC77107; AAC77107; b4147.
EnsemblBacteria; BAE78149; BAE78149; BAE78149.
GeneID; 948661; -.
KEGG; ecj:JW4107; -.
KEGG; eco:b4147; -.
PATRIC; fig|1411691.4.peg.2553; -.
EchoBASE; EB2023; -.
EcoGene; EG12099; efp.
eggNOG; ENOG4105DRH; Bacteria.
eggNOG; COG0231; LUCA.
HOGENOM; HOG000010047; -.
InParanoid; P0A6N4; -.
KO; K02356; -.
OMA; NTFSAGH; -.
PhylomeDB; P0A6N4; -.
BioCyc; EcoCyc:EG12099-MONOMER; -.
BioCyc; MetaCyc:EG12099-MONOMER; -.
UniPathway; UPA00345; -.
PRO; PR:P0A6N4; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005737; C:cytoplasm; IDA:EcoCyc.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0043022; F:ribosome binding; IDA:EcoCyc.
GO; GO:0003746; F:translation elongation factor activity; IDA:EcoCyc.
GO; GO:2001125; P:negative regulation of translational frameshifting; IMP:EcoCyc.
GO; GO:0072344; P:rescue of stalled ribosome; IMP:EcoCyc.
GO; GO:0006414; P:translational elongation; IDA:EcoCyc.
CDD; cd04470; S1_EF-P_repeat_1; 1.
CDD; cd05794; S1_EF-P_repeat_2; 1.
Gene3D; 2.30.30.30; -; 1.
HAMAP; MF_00141; EF_P; 1.
InterPro; IPR015365; Elong-fact-P_C.
InterPro; IPR012340; NA-bd_OB-fold.
InterPro; IPR014722; Rib_L2_dom2.
InterPro; IPR020599; Transl_elong_fac_P/YeiP.
InterPro; IPR013185; Transl_elong_KOW-like.
InterPro; IPR001059; Transl_elong_P/YeiP_cen.
InterPro; IPR013852; Transl_elong_P/YeiP_CS.
InterPro; IPR011768; Transl_elongation_fac_P.
InterPro; IPR008991; Translation_prot_SH3-like_sf.
PANTHER; PTHR30053; PTHR30053; 1.
Pfam; PF01132; EFP; 1.
Pfam; PF08207; EFP_N; 1.
Pfam; PF09285; Elong-fact-P_C; 1.
PIRSF; PIRSF005901; EF-P; 1.
SMART; SM01185; EFP; 1.
SMART; SM00841; Elong-fact-P_C; 1.
SUPFAM; SSF50104; SSF50104; 1.
SUPFAM; SSF50249; SSF50249; 2.
TIGRFAMs; TIGR00038; efp; 1.
PROSITE; PS01275; EFP; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Direct protein sequencing;
Elongation factor; Hydroxylation; Protein biosynthesis;
Reference proteome.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:1956781,
ECO:0000269|PubMed:9298646}.
CHAIN 2 188 Elongation factor P.
/FTId=PRO_0000094245.
MOD_RES 34 34 N6-(3,6-diaminohexanoyl)-5-hydroxylysine.
{ECO:0000269|PubMed:21841797,
ECO:0000269|PubMed:22128152,
ECO:0000269|PubMed:22706199}.
MUTAGEN 31 31 K->A: No lysylation.
{ECO:0000269|PubMed:20729861}.
MUTAGEN 33 33 G->K: No lysylation. Loss of in vivo EF-P
function for cell growth.
{ECO:0000269|PubMed:20729861}.
MUTAGEN 34 34 K->A: No lysylation and loss of EF-P
activity. No facilitation of translation
of poly-Pro stretches.
{ECO:0000269|PubMed:20729861,
ECO:0000269|PubMed:22128152,
ECO:0000269|PubMed:23239623}.
STRAND 4 6 {ECO:0000244|PDB:3A5Z}.
STRAND 14 17 {ECO:0000244|PDB:3A5Z}.
STRAND 20 30 {ECO:0000244|PDB:3A5Z}.
STRAND 38 45 {ECO:0000244|PDB:3A5Z}.
HELIX 46 48 {ECO:0000244|PDB:3A5Z}.
STRAND 51 57 {ECO:0000244|PDB:3A5Z}.
STRAND 61 64 {ECO:0000244|PDB:3A5Z}.
STRAND 67 70 {ECO:0000244|PDB:3A5Z}.
STRAND 73 77 {ECO:0000244|PDB:3A5Z}.
STRAND 82 85 {ECO:0000244|PDB:3A5Z}.
TURN 87 89 {ECO:0000244|PDB:3A5Z}.
STRAND 92 95 {ECO:0000244|PDB:3A5Z}.
HELIX 97 100 {ECO:0000244|PDB:3A5Z}.
TURN 102 106 {ECO:0000244|PDB:3A5Z}.
STRAND 109 112 {ECO:0000244|PDB:3A5Z}.
STRAND 114 118 {ECO:0000244|PDB:3A5Z}.
STRAND 121 126 {ECO:0000244|PDB:3A5Z}.
STRAND 152 156 {ECO:0000244|PDB:3A5Z}.
STRAND 161 164 {ECO:0000244|PDB:3A5Z}.
STRAND 173 177 {ECO:0000244|PDB:3A5Z}.
TURN 178 181 {ECO:0000244|PDB:3A5Z}.
STRAND 182 186 {ECO:0000244|PDB:3A5Z}.
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


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