EPMA_ECOLI
ID EPMA_ECOLI Reviewed; 325 AA.
AC P0A8N7; P03812; P78141; Q2M6E7; Q8XDP9;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Elongation factor P--(R)-beta-lysine ligase {ECO:0000255|HAMAP-Rule:MF_00174};
DE Short=EF-P--(R)-beta-lysine ligase {ECO:0000255|HAMAP-Rule:MF_00174};
DE EC=6.3.1.- {ECO:0000255|HAMAP-Rule:MF_00174};
DE AltName: Full=EF-P post-translational modification enzyme A {ECO:0000255|HAMAP-Rule:MF_00174};
DE AltName: Full=EF-P-lysine lysyltransferase {ECO:0000255|HAMAP-Rule:MF_00174};
DE AltName: Full=GX;
GN Name=epmA {ECO:0000255|HAMAP-Rule:MF_00174}; Synonyms=genX, poxA, yjeA;
GN OrderedLocusNames=b4155, JW4116;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1761227; DOI=10.1016/0378-1119(91)90503-4;
RA Kong L., Fromant M., Blanquet S., Plateau P.;
RT "Evidence for a new Escherichia coli protein resembling a lysyl-tRNA
RT synthetase.";
RL Gene 108:163-164(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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-152.
RX PubMed=7037404; DOI=10.1111/j.1432-1033.1982.tb06462.x;
RA Cole S.T.;
RT "Nucleotide sequence coding for the flavoprotein subunit of the fumarate
RT reductase of Escherichia coli.";
RL Eur. J. Biochem. 122:479-484(1982).
RN [6]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=6286595; DOI=10.1128/jb.151.3.1279-1289.1982;
RA Chang Y.-Y., Cronan J.E. Jr.;
RT "Mapping nonselectable genes of Escherichia coli by using transposon Tn10:
RT location of a gene affecting pyruvate oxidase.";
RL J. Bacteriol. 151:1279-1289(1982).
RN [7]
RP SIMILARITY TO CLASS-II AA-TRNA SYNTHETASES.
RX PubMed=2668951; DOI=10.1073/pnas.86.16.6023;
RA Gampel A., Tzagoloff A.;
RT "Homology of aspartyl- and lysyl-tRNA synthetases.";
RL Proc. Natl. Acad. Sci. U.S.A. 86:6023-6027(1989).
RN [8]
RP CRYSTALLIZATION, AND SUBUNIT.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=20823541; DOI=10.1107/s1744309110032008;
RA Sumida T., Yanagisawa T., Ishii R., Yokoyama S.;
RT "Crystallization and preliminary X-ray crystallographic study of GenX, a
RT lysyl-tRNA synthetase paralogue from Escherichia coli, in complex with
RT translation elongation factor P.";
RL Acta Crystallogr. F 66:1115-1118(2010).
RN [9]
RP POSSIBLE FUNCTION.
RX PubMed=20070887; DOI=10.1186/1745-6150-5-3;
RA Bailly M., de Crecy-Lagard V.;
RT "Predicting the pathway involved in post-translational modification of
RT Elongation factor P in a subset of bacterial species.";
RL Biol. Direct 5:3-3(2010).
RN [10]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS,
RP AND MUTAGENESIS OF SER-76 AND ALA-298.
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 FUNCTION IN EF-P BETA-LYSYLATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
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 GENE NAME, AND PATHWAY.
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 DISRUPTION PHENOTYPE.
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 X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEXES WITH LYSYL-ADENYLATE
RP ANALOG AND EF-P, FUNCTION IN EF-P LYSYLATION, SUBUNIT, DISRUPTION
RP PHENOTYPE, AND MUTAGENESIS OF ASP-50; ARG-100; GLU-102; GLU-103; HIS-108;
RP GLU-185; GLN-193; GLU-244; ASN-247 AND ARG-303.
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: With EpmB is involved in the beta-lysylation step of the
CC post-translational modification of translation elongation factor P (EF-
CC P) on 'Lys-34'. Catalyzes the ATP-dependent activation of (R)-beta-
CC lysine produced by EpmB, forming a lysyl-adenylate, from which the
CC beta-lysyl moiety is then transferred to the epsilon-amino group of EF-
CC P 'Lys-34'. The substrate (R)-beta-lysine is 100-fold more efficient
CC than either (S)-beta-lysine or L-alpha-lysine. Cannot ligate lysine to
CC any tRNA. {ECO:0000255|HAMAP-Rule:MF_00174,
CC ECO:0000269|PubMed:20729861, ECO:0000269|PubMed:21841797,
CC ECO:0000269|PubMed:22128152}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=213 uM for (R)-beta-lysine {ECO:0000269|PubMed:21841797};
CC KM=8600 uM for L-alpha-lysine {ECO:0000269|PubMed:21841797};
CC KM=6950 uM for (S)-beta-lysine {ECO:0000269|PubMed:21841797};
CC KM=206 uM for ATP {ECO:0000269|PubMed:21841797};
CC Note=kcat is 36 min(-1) for the amino acid activation reaction with
CC (R)-beta-lysine as substrate.;
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00174,
CC ECO:0000269|PubMed:20729861, ECO:0000269|PubMed:20823541}.
CC -!- INTERACTION:
CC P0A8N7; P0AFG8: aceE; NbExp=2; IntAct=EBI-562598, EBI-542683;
CC -!- DISRUPTION PHENOTYPE: Cells have a reduced pyruvate oxidase activity
CC and a reduced growth rate. Cells lack CadA activity (lysine
CC decarboxylase). {ECO:0000269|PubMed:20729861,
CC ECO:0000269|PubMed:23239623, ECO:0000269|PubMed:6286595}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC EpmA subfamily. {ECO:0000255|HAMAP-Rule:MF_00174}.
CC -!- CAUTION: Was originally suggested to be a tRNA synthase, however its
CC lack of an anticodon-binding domain made this highly unlikely.
CC {ECO:0000305|PubMed:1761227}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA97054.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; X59988; CAA42604.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97054.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC77115.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE78159.1; -; Genomic_DNA.
DR EMBL; J01611; AAA23436.2; -; Genomic_DNA.
DR PIR; S56383; S56383.
DR RefSeq; NP_418579.2; NC_000913.3.
DR RefSeq; WP_000004771.1; NZ_STEB01000014.1.
DR PDB; 3A5Y; X-ray; 1.90 A; A/B/C/D=1-325.
DR PDB; 3A5Z; X-ray; 2.50 A; A/C/E/G=1-325.
DR PDBsum; 3A5Y; -.
DR PDBsum; 3A5Z; -.
DR AlphaFoldDB; P0A8N7; -.
DR SMR; P0A8N7; -.
DR BioGRID; 4260877; 6.
DR DIP; DIP-10535N; -.
DR IntAct; P0A8N7; 3.
DR STRING; 511145.b4155; -.
DR jPOST; P0A8N7; -.
DR PaxDb; P0A8N7; -.
DR PRIDE; P0A8N7; -.
DR EnsemblBacteria; AAC77115; AAC77115; b4155.
DR EnsemblBacteria; BAE78159; BAE78159; BAE78159.
DR GeneID; 66671931; -.
DR GeneID; 948672; -.
DR KEGG; ecj:JW4116; -.
DR KEGG; eco:b4155; -.
DR PATRIC; fig|1411691.4.peg.2543; -.
DR EchoBASE; EB1196; -.
DR eggNOG; COG2269; Bacteria.
DR HOGENOM; CLU_008255_1_1_6; -.
DR InParanoid; P0A8N7; -.
DR OMA; EWYRPGF; -.
DR PhylomeDB; P0A8N7; -.
DR BioCyc; EcoCyc:EG11211-MON; -.
DR BioCyc; MetaCyc:EG11211-MON; -.
DR PRO; PR:P0A8N7; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0016880; F:acid-ammonia (or amide) ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004824; F:lysine-tRNA ligase activity; IBA:GO_Central.
DR GO; GO:0052868; F:protein-lysine lysyltransferase activity; IDA:EcoCyc.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0071468; P:cellular response to acidic pH; IMP:EcoCyc.
DR GO; GO:0006430; P:lysyl-tRNA aminoacylation; IBA:GO_Central.
DR GO; GO:0071915; P:protein-lysine lysylation; IDA:EcoCyc.
DR GO; GO:0072581; P:protein-N6-(L-lysyl)-L-lysine modification to protein-N6-(beta-lysyl)-L-lysine; IDA:EcoCyc.
DR Gene3D; 3.30.930.10; -; 1.
DR HAMAP; MF_00174; EF_P_modif_A; 1.
DR InterPro; IPR004364; Aa-tRNA-synt_II.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR004525; EpmA.
DR InterPro; IPR018149; Lys-tRNA-synth_II_C.
DR Pfam; PF00152; tRNA-synt_2; 1.
DR PRINTS; PR00982; TRNASYNTHLYS.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00462; genX; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Ligase; Nucleotide-binding; Reference proteome.
FT CHAIN 1..325
FT /note="Elongation factor P--(R)-beta-lysine ligase"
FT /id="PRO_0000152719"
FT BINDING 76..78
FT /ligand="substrate"
FT BINDING 100..102
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 109
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 118
FT /ligand="substrate"
FT BINDING 244..245
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 251
FT /ligand="substrate"
FT BINDING 300
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT MUTAGEN 50
FT /note="D->A: No effect on lysylation activity."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 76
FT /note="S->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:21841797"
FT MUTAGEN 100
FT /note="R->A: Loss of lysylation activity."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 102
FT /note="E->A: No effect on lysylation activity."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 103
FT /note="E->A: Loss of lysylation activity."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 108
FT /note="H->A: Severe reduction in lysylation activity."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 185
FT /note="E->A: Slight reduction in lysylation activity."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 193
FT /note="Q->A: Slight reduction in lysylation activity."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 244
FT /note="E->A: Loss of lysylation activity."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 247
FT /note="N->A: Loss of lysylation activity."
FT /evidence="ECO:0000269|PubMed:20729861"
FT MUTAGEN 298
FT /note="A->G: 96% increase in the affinity for L-alpha-
FT lysine. 4-fold decrease in the catalytic efficiency of the
FT (R)-beta-lysine activation reaction."
FT /evidence="ECO:0000269|PubMed:21841797"
FT MUTAGEN 303
FT /note="R->A: Loss of lysylation activity."
FT /evidence="ECO:0000269|PubMed:20729861"
FT CONFLICT 78
FT /note="E -> Q (in Ref. 5; AAA23436)"
FT /evidence="ECO:0000305"
FT CONFLICT 144
FT /note="A -> E (in Ref. 5; AAA23436)"
FT /evidence="ECO:0000305"
FT HELIX 13..32
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 42..46
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 57..60
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 63..65
FT /evidence="ECO:0007829|PDB:3A5Z"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 78..86
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 91..99
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 110..120
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 124..139
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 145..148
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 149..156
FT /evidence="ECO:0007829|PDB:3A5Y"
FT TURN 161..163
FT /evidence="ECO:0007829|PDB:3A5Z"
FT HELIX 166..170
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 172..175
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 179..182
FT /evidence="ECO:0007829|PDB:3A5Z"
FT HELIX 190..199
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 201..203
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 204..208
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 210..213
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 217..219
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 232..240
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 243..251
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 255..271
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 281..289
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 293..300
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 301..309
FT /evidence="ECO:0007829|PDB:3A5Y"
FT HELIX 314..317
FT /evidence="ECO:0007829|PDB:3A5Y"
FT STRAND 318..320
FT /evidence="ECO:0007829|PDB:3A5Y"
FT TURN 322..324
FT /evidence="ECO:0007829|PDB:3A5Y"
SQ SEQUENCE 325 AA; 36976 MW; F72B535CCA23E4CC CRC64;
MSETASWQPS ASIPNLLKRA AIMAEIRRFF ADRGVLEVET PCMSQATVTD IHLVPFETRF
VGPGHSQGMN LWLMTSPEYH MKRLLVAGCG PVFQLCRSFR NEEMGRYHNP EFTMLEWYRP
HYDMYRLMNE VDDLLQQVLD CPAAESLSYQ QAFLRYLEID PLSADKTQLR EVAAKLDLSN
VADTEEDRDT LLQLLFTFGV EPNIGKEKPT FVYHFPASQA SLAQISTEDH RVAERFEVYY
KGIELANGFH ELTDAREQQQ RFEQDNRKRA ARGLPQHPID QNLIEALKVG MPDCSGVALG
VDRLVMLALG AETLAEVIAF SVDRA
