EPMA_SALTY
ID EPMA_SALTY Reviewed; 325 AA.
AC Q9ZJ12;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2002, sequence version 2.
DT 03-AUG-2022, entry version 127.
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};
GN Name=epmA {ECO:0000255|HAMAP-Rule:MF_00174}; Synonyms=genX, yjeA;
GN OrderedLocusNames=STM4344;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND DISRUPTION PHENOTYPE.
RC STRAIN=UK-1;
RX PubMed=9826331; DOI=10.1128/iai.66.12.5599-5606.1998;
RA Kaniga K., Compton M.S., Curtiss R. III, Sundaram P.;
RT "Molecular and functional characterization of Salmonella enterica serovar
RT typhimurium poxA gene: effect on attenuation of virulence and protection.";
RL Infect. Immun. 66:5599-5606(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH AMP AND PHOSPHATE,
RP FUNCTION IN EF-P MODIFICATION, LYSYLATION ACTIVITY, SUBUNIT, DISRUPTION
RP PHENOTYPE, AND MUTAGENESIS OF SER-76; GLU-78; ARG-100; GLU-102; HIS-108;
RP PHE-112; GLU-116; TYR-118; GLU-244 AND ARG-303.
RC STRAIN=14028s / SGSC 2262, and LT2 / SGSC1412 / ATCC 700720;
RX PubMed=20670890; DOI=10.1016/j.molcel.2010.06.021;
RA Navarre W.W., Zou S.B., Roy H., Xie J.L., Savchenko A., Singer A.,
RA Edvokimova E., Prost L.R., Kumar R., Ibba M., Fang F.C.;
RT "PoxA, YjeK, and elongation factor P coordinately modulate virulence and
RT drug resistance in Salmonella enterica.";
RL Mol. Cell 39:209-221(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' (Probable). Can also use L-alpha-lysine as a substrate, but
CC probably with lower efficiency. Cannot aminoacylate tRNA(Lys) with
CC lysine. {ECO:0000255|HAMAP-Rule:MF_00174, ECO:0000269|PubMed:20670890,
CC ECO:0000305}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00174,
CC ECO:0000269|PubMed:20670890}.
CC -!- DISRUPTION PHENOTYPE: Mutants have a reduced pyruvate oxidase activity
CC and a reduced growth rate, and are highly attenuated for virulence in
CC mouse models of infection. Salmonella epmA and epmB mutants share
CC extensive phenotypic pleiotropy, including an increased ability to
CC respire under nutrient-limiting conditions, hypersusceptibility to a
CC variety of diverse growth inhibitors, and altered expression of
CC multiple proteins, including several encoded on the SPI-1 pathogenicity
CC island. {ECO:0000269|PubMed:20670890, ECO:0000269|PubMed:9826331}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC EpmA subfamily. {ECO:0000255|HAMAP-Rule:MF_00174}.
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DR EMBL; AF001831; AAC82540.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL23167.1; -; Genomic_DNA.
DR RefSeq; NP_463208.1; NC_003197.2.
DR RefSeq; WP_000004794.1; NC_003197.2.
DR PDB; 3G1Z; X-ray; 1.95 A; A/B=1-325.
DR PDBsum; 3G1Z; -.
DR AlphaFoldDB; Q9ZJ12; -.
DR SMR; Q9ZJ12; -.
DR STRING; 99287.STM4344; -.
DR PaxDb; Q9ZJ12; -.
DR EnsemblBacteria; AAL23167; AAL23167; STM4344.
DR GeneID; 1255870; -.
DR KEGG; stm:STM4344; -.
DR PATRIC; fig|99287.12.peg.4571; -.
DR HOGENOM; CLU_008255_1_1_6; -.
DR OMA; EWYRPGF; -.
DR PhylomeDB; Q9ZJ12; -.
DR EvolutionaryTrace; Q9ZJ12; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
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:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0006430; P:lysyl-tRNA aminoacylation; IBA:GO_Central.
DR GO; GO:0071915; P:protein-lysine lysylation; IEA:UniProtKB-UniRule.
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_0000152728"
FT BINDING 76..78
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00174"
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 /evidence="ECO:0000255|HAMAP-Rule:MF_00174"
FT BINDING 244..245
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 251
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00174"
FT BINDING 300
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00174"
FT MUTAGEN 76
FT /note="S->A: Partial loss of activity."
FT /evidence="ECO:0000269|PubMed:20670890"
FT MUTAGEN 78
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:20670890"
FT MUTAGEN 100
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:20670890"
FT MUTAGEN 102
FT /note="E->A: No effect on activity."
FT /evidence="ECO:0000269|PubMed:20670890"
FT MUTAGEN 108
FT /note="H->A: No effect on activity."
FT /evidence="ECO:0000269|PubMed:20670890"
FT MUTAGEN 112
FT /note="F->A: Partial loss of activity."
FT /evidence="ECO:0000269|PubMed:20670890"
FT MUTAGEN 116
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:20670890"
FT MUTAGEN 118
FT /note="Y->A: No effect on activity."
FT /evidence="ECO:0000269|PubMed:20670890"
FT MUTAGEN 244
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:20670890"
FT MUTAGEN 303
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:20670890"
FT CONFLICT 31
FT /note="A -> G (in Ref. 1; AAC82540)"
FT /evidence="ECO:0000305"
FT CONFLICT 86
FT /note="A -> E (in Ref. 1; AAC82540)"
FT /evidence="ECO:0000305"
FT CONFLICT 158
FT /note="E -> G (in Ref. 1; AAC82540)"
FT /evidence="ECO:0000305"
FT CONFLICT 275
FT /note="P -> A (in Ref. 1; AAC82540)"
FT /evidence="ECO:0000305"
FT CONFLICT 279
FT /note="I -> M (in Ref. 1; AAC82540)"
FT /evidence="ECO:0000305"
FT HELIX 13..32
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 42..46
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 57..60
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 78..87
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 91..99
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 110..120
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 124..139
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 145..148
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 149..157
FT /evidence="ECO:0007829|PDB:3G1Z"
FT TURN 161..163
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 166..175
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 179..184
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 188..199
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 201..203
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 204..208
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 210..213
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 217..219
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 232..240
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 243..251
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 255..271
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 281..289
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 294..300
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 301..309
FT /evidence="ECO:0007829|PDB:3G1Z"
FT HELIX 314..316
FT /evidence="ECO:0007829|PDB:3G1Z"
FT STRAND 318..320
FT /evidence="ECO:0007829|PDB:3G1Z"
FT TURN 322..324
FT /evidence="ECO:0007829|PDB:3G1Z"
SQ SEQUENCE 325 AA; 36856 MW; E90A3109EE388E4C CRC64;
MSETATWQPS ASIPNLLKRA AIMAEIRRFF ADRGVLEVET PCMSQATVTD IHLFPFETRF
VGPGHSQGIN LYLMTSPEYH MKRLLAAGCG PVFQLCRSFR NEEMGRHHNP EFTMLEWYRP
HYDMYRLMNE VDDLLQQVLD CQPAESLSYQ QAFQRHLEID PLSADKTQLR EAAAKLDLSN
IADTEEDRDT LLQLLFTMGV EPHIGKEKPT FIYHFPASQA SLAQISTEDH RVAERFEVYY
KGIELANGFH ELTDAREQQQ RFEQDNRKRA ARGLPQQPID QNLLDALAAG LPDCSGVALG
VDRLVMLALG AESLADVIAF TVDRA
