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Escherichia coli K-12 substr. MG1655 Enzyme: lysine 2,3-aminomutase

Gene: epmB Accession Numbers: G7836 (EcoCyc), b4146, ECK4140

Synonyms: yjeK

Regulation Summary Diagram: ?

Regulation summary diagram for epmB

Co-expression of EpmB enhances the lysylation of EF-P by EpmA in vivo. EpmB may catalyze the conversion of α-lysyl-EF-P to β-lysyl-EF-P [Yanagisawa10], but preliminary evidence indicates that it acts before EpmA [Park12b].

The epmB gene product is similar to the lysine 2,3-aminomutase of Clostridium subterminale, although phylogenetic clustering has shown that EpmB belongs to a different subfamily than the lysine 2,3-aminomutases [Bailly10]. The purified protein has low lysine 2,3-aminomutase activity and produces (R)-β-lysine, the enantiomer of the product of the Clostridium enzyme. The low activity of the E. coli enzyme compared to the clostridial enzyme may indicate that L-lysine is not its natural substrate, or that β-lysine is required in low amounts [Behshad06]. EpmB is a member of the "radical SAM" family of enzymes, and the lysyl-free radical intermediate of the reaction has been characterized [Behshad06].

Physical clustering and phylogenetic analysis have implicated EpmB in a pathway for the modification of a lysine residue in protein chain elongation factor EF-P [Bailly10].

EpmB: "EF-P post-translational modification B" [Peil12]

Locations: cytosol

Map Position: [4,372,652 <- 4,373,680] (94.24 centisomes, 339°)
Length: 1029 bp / 342 aa

Molecular Weight of Polypeptide: 38.75 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013580 , EchoBASE:EB2366 , EcoGene:EG12473 , EcoliWiki:b4146 , ModBase:P39280 , OU-Microarray:b4146 , PortEco:yjeK , Pride:P39280 , Protein Model Portal:P39280 , RefSeq:NP_418570 , RegulonDB:G7836 , SMR:P39280 , String:511145.b4146 , UniProt:P39280

Relationship Links: InterPro:IN-FAMILY:IPR003739 , InterPro:IN-FAMILY:IPR007197 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR022462 , Pfam:IN-FAMILY:PF04055

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0043687 - post-translational protein modification Inferred by computational analysis [Bailly10]
Molecular Function: GO:0016869 - intramolecular transferase activity, transferring amino groups Inferred from experiment [Behshad06]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Behshad06]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: regulation type of regulation posttranscriptional covalent modification, demodification, maturation

Essentiality data for epmB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Last-Curated ? 16-Dec-2011 by Keseler I , SRI International

Enzymatic reaction of: lysine 2,3-aminomutase

EC Number: 5.4.3.-

L-lysine <=> (R)-β-lysine

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.

The kcat value of the E. coli enzyme is 0.1% of that of the clostridial enzyme [Behshad06].

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Behshad06], pyridoxal 5'-phosphate [Behshad06], S-adenosyl-L-methionine [Behshad06]

Kinetic Parameters:

Km (μM)

Sequence Features

Protein sequence of lysine 2,3-aminomutase with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 120
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: potential;
Metal-Binding-Site 124
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: potential;
Metal-Binding-Site 127
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: potential;
N6-pyridoxal-phosphate-Lys-Modification 332
UniProt: N6-(pyridoxal phosphate)lysine; Non-Experimental Qualifier: by similarity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bailly10: Bailly M, de Crecy-Lagard V (2010). "Predicting the pathway involved in post-translational modification of Elongation factor P in a subset of bacterial species." Biol Direct 5(1);3. PMID: 20070887

Behshad06: Behshad E, Ruzicka FJ, Mansoorabadi SO, Chen D, Reed GH, Frey PA (2006). "Enantiomeric free radicals and enzymatic control of stereochemistry in a radical mechanism: the case of lysine 2,3-aminomutases." Biochemistry 45(42);12639-46. PMID: 17042480

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Park12b: Park JH, Johansson HE, Aoki H, Huang BX, Kim HY, Ganoza MC, Park MH (2012). "Post-translational modification by β-lysylation is required for activity of Escherichia coli elongation factor P (EF-P)." J Biol Chem 287(4);2579-90. PMID: 22128152

Peil12: Peil L, Starosta AL, Virumae K, Atkinson GC, Tenson T, Remme J, Wilson DN (2012). "Lys34 of translation elongation factor EF-P is hydroxylated by YfcM." Nat Chem Biol 8(8);695-7. PMID: 22706199

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-11 released on 2012-11-26 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Yanagisawa10: Yanagisawa T, Sumida T, Ishii R, Takemoto C, Yokoyama S (2010). "A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P." Nat Struct Mol Biol 17(9);1136-43. PMID: 20729861

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Tue Sep 1, 2015, biocyc11.