|Gene:||epmB||Accession Numbers: G7836 (EcoCyc), b4146, ECK4140|
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 [Park12a].
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].
EpmB: "EF-P post-translational modification B" [Peil12]
|Map Position: [4,372,652 <- 4,373,680] (94.24 centisomes)||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
|Biological Process:||GO:0043687 - post-translational protein modification [Bailly10]|
|Molecular Function:||GO:0016869 - intramolecular transferase activity, transferring amino groups
GO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a, Behshad06]
GO:0003824 - catalytic activity [GOA01a]
GO:0016853 - isomerase activity [UniProtGOA11a]
GO:0046872 - metal ion binding [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding [UniProtGOA11a, GOA01a]
|Cellular Component:||GO:0005829 - cytosol [DiazMejia09]|
|MultiFun Terms:||regulation → type of regulation → posttranscriptional → covalent modification, demodification, maturation|
|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]|
Enzymatic reaction of: lysine 2,3-aminomutase
EC Number: 5.4.3.-
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].
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
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
Park12a: 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
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
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