EPMB_ECOLI
ID EPMB_ECOLI Reviewed; 342 AA.
AC P39280; Q2M6F8;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=L-lysine 2,3-aminomutase;
DE Short=LAM;
DE EC=5.4.3.-;
DE AltName: Full=EF-P post-translational modification enzyme B;
GN Name=epmB; Synonyms=yjeK; OrderedLocusNames=b4146, JW4106;
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=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 [2]
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 [3]
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 [4]
RP FUNCTION AS A LYSINE 2,3-AMINOMUTASE, CATALYTIC ACTIVITY, COFACTOR, KINETIC
RP PARAMETERS, AND REACTION MECHANISM.
RX PubMed=17042480; DOI=10.1021/bi061328t;
RA Behshad E., Ruzicka F.J., Mansoorabadi S.O., Chen D., Reed G.H., Frey P.A.;
RT "Enantiomeric free radicals and enzymatic control of stereochemistry in a
RT radical mechanism: the case of lysine 2,3-aminomutases.";
RL Biochemistry 45:12639-12646(2006).
RN [5]
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 [6]
RP FUNCTION IN EF-P LYSYLATION.
RC STRAIN=K12;
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).
RN [7]
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 [8]
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 [9]
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).
CC -!- FUNCTION: With EpmA is involved in the beta-lysylation step of the
CC post-translational modification of translation elongation factor P (EF-
CC P) on 'Lys-34'. EpmB appears to act before EpmA. Displays lysine 2,3-
CC aminomutase activity, producing (R)-beta-lysine from (S)-alpha-lysine
CC (L-lysine). Cannot use (S)-ornithine or (R)-alpha-lysine as a
CC substrate. {ECO:0000269|PubMed:17042480, ECO:0000269|PubMed:20729861,
CC ECO:0000269|PubMed:22128152}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysine = D-beta-lysine; Xref=Rhea:RHEA:44148,
CC ChEBI:CHEBI:32551, ChEBI:CHEBI:84138;
CC Evidence={ECO:0000269|PubMed:17042480};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:17042480};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000269|PubMed:17042480};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:17042480};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=5 mM for L-lysine (at pH 8 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:17042480};
CC Note=kcat is 4.8 min(-1) (at pH 8 and 25 degrees Celsius).;
CC -!- DISRUPTION PHENOTYPE: Cells lack CadA activity (lysine decarboxylase).
CC {ECO:0000269|PubMed:23239623}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. KamA family.
CC {ECO:0000305}.
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DR EMBL; U14003; AAA97045.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77106.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78148.1; -; Genomic_DNA.
DR PIR; S56374; S56374.
DR RefSeq; NP_418570.1; NC_000913.3.
DR RefSeq; WP_000940549.1; NZ_LN832404.1.
DR AlphaFoldDB; P39280; -.
DR SMR; P39280; -.
DR BioGRID; 852954; 1.
DR IntAct; P39280; 16.
DR STRING; 511145.b4146; -.
DR jPOST; P39280; -.
DR PaxDb; P39280; -.
DR PRIDE; P39280; -.
DR EnsemblBacteria; AAC77106; AAC77106; b4146.
DR EnsemblBacteria; BAE78148; BAE78148; BAE78148.
DR GeneID; 948662; -.
DR KEGG; ecj:JW4106; -.
DR KEGG; eco:b4146; -.
DR PATRIC; fig|1411691.4.peg.2554; -.
DR EchoBASE; EB2366; -.
DR eggNOG; COG1509; Bacteria.
DR HOGENOM; CLU_032161_2_0_6; -.
DR InParanoid; P39280; -.
DR OMA; PIWLNTH; -.
DR PhylomeDB; P39280; -.
DR BioCyc; EcoCyc:G7836-MON; -.
DR BioCyc; MetaCyc:G7836-MON; -.
DR PRO; PR:P39280; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0016869; F:intramolecular transferase activity, transferring amino groups; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR022462; EpmB.
DR InterPro; IPR003739; Lys_aminomutase/Glu_NH3_mut.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR30538; PTHR30538; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR PIRSF; PIRSF004911; DUF160; 1.
DR SFLD; SFLDF00314; L-lysine_2_3-aminomutase_(yjeK; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR TIGRFAMs; TIGR03821; EFP_modif_epmB; 1.
DR TIGRFAMs; TIGR00238; TIGR00238; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Iron; Iron-sulfur; Isomerase; Metal-binding; Pyridoxal phosphate;
KW Reference proteome; S-adenosyl-L-methionine.
FT CHAIN 1..342
FT /note="L-lysine 2,3-aminomutase"
FT /id="PRO_0000172288"
FT DOMAIN 106..329
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 120
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 124
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 127
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT MOD_RES 332
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
SQ SEQUENCE 342 AA; 38750 MW; C35F066281588CD3 CRC64;
MAHIVTLNTP SREDWLTQLA DVVTDPDELL RLLNIDAEEK LLAGRSAKKL FALRVPRSFI
DRMEKGNPDD PLLRQVLTSQ DEFVIAPGFS TDPLEEQHSV VPGLLHKYHN RALLLVKGGC
AVNCRYCFRR HFPYAENQGN KRNWQTALEY VAAHPELDEM IFSGGDPLMA KDHELDWLLT
QLEAIPHIKR LRIHSRLPIV IPARITEALV ECFARSTLQI LLVNHINHAN EVDETFRQAM
AKLRRVGVTL LNQSVLLRDV NDNAQTLANL SNALFDAGVM PYYLHVLDKV QGAAHFMVSD
DEARQIMREL LTLVSGYLVP KLAREIGGEP SKTPLDLQLR QQ
