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1. Petrovich  RM, Ruzicka  FJ, Reed  GH, Frey  PA,     ( 1992 )

Characterization of iron-sulfur clusters in lysine 2,3-aminomutase by electron paramagnetic resonance spectroscopy.

Biochemistry 31 (44)
PMID : 1329954  :   DOI  :   10.1021/bi00159a019    
Abstract >>
Lysine 2,3-aminomutase from Clostridia catalyzes the interconversion of L-alpha-lysine with L-beta-lysine. The purified enzyme contains iron-sulfur ([Fe-S]) clusters, pyridoxal phosphate, and Co(II) [Petrovich, R. M., Ruzicka, F. J., Reed, G. H., & Frey, P. A. (1991) J. Biol. Chem. 266, 7656-7660]. Enzymatic activity depends upon the presence and integrity of these cofactors. In addition, the enzyme is activated by S-adenosylmethionine, which participates in the transfer of a substrate hydrogen atom between carbon-3 of lysine and carbon-2 of beta-lysine [Moss, M., & Frey, P. A. (1987) J. Biol. Chem. 262, 14859-14862]. This paper describes the electron paramagnetic resonance (EPR) properties of the [Fe-S] clusters. Purified samples of the enzyme also contain low and variable levels of a stable radical. The radical spectrum is centered at g = 2.006 and is subject to inhomogeneous broadening at 10 K, with a p1/2 value of 550 +/- 100 microW. The low-temperature EPR spectrum of the [Fe-S] cluster is centered at g = 2.007 and undergoes power saturation at 10 K in a homogeneous manner, with a p1/2 of 15 +/- 2 mW. The signals are consistent with the formulation [4Fe-4S] and are adequately simulated by a rhombic spectrum, in which gxx = 2.027, gyy = 2.007, and gzz = 1.99. Treatment of the enzyme with reducing agents converts the cluster into an EPR-silent form. Oxidation of the purified enzyme by air or ferricyanide converts the [Fe-S] complex into a species with an EPR spectrum that is consistent with the formulation [3Fe-4S].(ABSTRACT TRUNCATED AT 250 WORDS)
KeywordMeSH Terms
Electron Spin Resonance Spectroscopy
Intramolecular Transferases
2. Miller  J, Bandarian  V, Reed  GH, Frey  PA,     ( 2001 )

Inhibition of lysine 2,3-aminomutase by the alternative substrate 4-thialysine and characterization of the 4-thialysyl radical intermediate.

Archives of biochemistry and biophysics 387 (2)
PMID : 11370852  :   DOI  :   10.1006/abbi.2001.2261    
Abstract >>
Lysine 2,3-aminomutase catalyzes the interconversion of L-lysine and L-beta-lysine. 4-Thia-L-lysine (4-thialysine) is an alternative substrate for Lysine 2,3-aminomutase. The organic free radical that appears in the steady state of the reaction of 4-thialysine is structurally analogous to the first lysine-based radical in the chemical mechanism (Wu, W., Lieder, K. W., Reed, G. H., and Frey, P. A. (1995) Biochemistry 34, 10532-10537). 4-Thialysine is a much more potent inhibitor of the reaction of lysine than would be anticipated on the basis of the value of Km for its reaction as a substrate. 4-Thialysine is here shown to be a competitive reversible inhibitor with respect to L-lysine, displaying an inhibition constant of 0.12 +/- 0.01 mM. The value of Km for 4-thialysine is 1.4 +/- 0.1 mM, and the maximum velocity Vm = 0.19 +/-0.02 micromol min(-1) mg-1 at 37 degrees C and pH 8.0. The kinetic parameters for the reaction of lysine under the same conditions are: Km = 4.2 +/- 0.5 mM and Vm = 43 +/- 1 micromol min(-1) mg(-1). The discrepancy between Km and the apparent Ki for 4-thialysine arises from the fact that the maximal velocity for 4-thialysine is only 0.44% that for L-lysine. The electron paramagnetic resonance spectra of the organic radical generated at the active site from 4-thialysine and those generated from deuterium and 3-13C-labeled forms of 4-thialysine were analyzed by simulation. Based on the resulting hyperfine splitting constants, the conformation and distribution of the unpaired spin of the radical at the active site were evaluated.
KeywordMeSH Terms
3. Lieder  KW, Ruzicka  FJ,     ( 2000 )

Lysine 2,3-aminomutase from Clostridium subterminale SB4: mass spectral characterization of cyanogen bromide-treated peptides and cloning, sequencing, and expression of the gene kamA in Escherichia coli.

Journal of bacteriology 182 (2)
PMID : 10629195  :   DOI  :   10.1128/jb.182.2.469-476.2000     PMC  :   PMC94298    
Abstract >>
Lysine 2,3-aminomutase (KAM, EC catalyzes the interconversion of L-lysine and L-beta-lysine, the first step in lysine degradation in Clostridium subterminale SB4. KAM requires S-adenosylmethionine (SAM), which mediates hydrogen transfer in a mechanism analogous to adenosylcobalamin-dependent reactions. KAM also contains an iron-sulfur cluster and requires pyridoxal 5'-phosphate (PLP) for activity. In the present work, we report the cloning and nucleotide sequencing of the gene kamA for C. subterminale SB4 KAM and conditions for its expression in Escherichia coli. The cyanogen bromide peptides were isolated and characterized by mass spectral analysis and, for selected peptides, amino acid and N-terminal amino acid sequence analysis. PCR was performed with degenerate oligonucleotide primers and C. subterminale SB4 chromosomal DNA to produce a portion of kamA containing 1,029 base pairs of the gene. The complete gene was obtained from a genomic library of C. subterminale SB4 chromosomal DNA by use of DNA probe analysis based on the 1,029-base pair fragment. The full-length gene consisted of 1,251 base pairs specifying a protein of 47,030 Da, in reasonable agreement with 47, 173 Da obtained by electrospray mass spectrometry of the purified enzyme. N- and C-terminal amino acid analysis of KAM and its cyanogen bromide peptides firmly correlated its amino acid sequence with the nucleotide sequence of kamA. A survey of bacterial genome databases identified seven homologs with 31 to 72% sequence identity to KAM, none of which were known enzymes. An E. coli expression system consisting of pET 23a(+) plus kamA yielded unsatisfactory expression and bacterial growth. Codon usage in kamA includes the use of AGA for all 29 arginine residues. AGA is rarely used in E. coli, and arginine clusters at positions 4 and 5, 25 and 27, and 134, 135, and 136 apparently compound the barrier to expression. Coexpression of E. coli argU dramatically enhanced both cell growth and expression of KAM. Purified recombinant KAM is equivalent to that purified from C. subterminale SB4.
KeywordMeSH Terms
4. Chen  D, Frey  PA, Lepore  BW, Ringe  D, Ruzicka  FJ,     ( 2006 )

Identification of structural and catalytic classes of highly conserved amino acid residues in lysine 2,3-aminomutase.

Biochemistry 45 (42)
PMID : 17042481  :   DOI  :   10.1021/bi061329l     PMC  :   PMC2527744    
Abstract >>
Lysine 2,3-aminomutase (LAM) from Clostridium subterminale SB4 catalyzes the interconversion of (S)-lysine and (S)-beta-lysine by a radical mechanism involving coenzymatic actions of S-adenosylmethionine (SAM), a [4Fe-4S] cluster, and pyridoxal 5'-phosphate (PLP). The enzyme contains a number of conserved acidic residues and a cysteine- and arginine-rich motif, which binds iron and sulfide in the [4Fe-4S] cluster. The results of activity and iron, sulfide, and PLP analysis of variants resulting from site-specific mutations of the conserved acidic residues and the arginine residues in the iron-sulfide binding motif indicate two classes of conserved residues of each type. Mutation of the conserved residues Arg134, Asp293, and Asp330 abolishes all enzymatic activity. On the basis of the X-ray crystal structure, these residues bind the epsilon-aminium and alpha-carboxylate groups of (S)-lysine. However, among these residues, only Asp293 appears to be important for stabilizing the [4Fe-4S] cluster. Members of a second group of conserved residues appear to stabilize the structure of LAM. Mutations of arginine 130, 135, and 136 and acidic residues Glu86, Asp165, Glu236, and Asp172 dramatically decrease iron and sulfide contents in the purified variants. Mutation of Asp96 significantly decreases iron and sulfide content. Arg130 or Asp172 variants display no detectable activity, whereas variants mutated at the other positions display low to very low activities. Structural roles are assigned to this latter class of conserved amino acids. In particular, a network of hydrogen bonded interactions of Arg130, Glu86, Arg135, and the main chain carbonyl groups of Cys132 and Leu55 appears to stabilize the [4Fe-4S] cluster.
KeywordMeSH Terms
5. Lepore  BW, Ruzicka  FJ, Frey  PA, Ringe  D,     ( 2005 )

The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale.

Proceedings of the National Academy of Sciences of the United States of America 102 (39)
PMID : 16166264  :   DOI  :   10.1073/pnas.0505726102     PMC  :   PMC1236562    
Abstract >>
The x-ray crystal structure of the pyridoxal-5'-phosphate (PLP), S-adenosyl-L-methionine (SAM), and [4Fe-4S]-dependent lysine-2,3-aminomutase (LAM) of Clostridium subterminale has been solved to 2.1-A resolution by single-wavelength anomalous dispersion methods on a L-selenomethionine-substituted complex of LAM with [4Fe-4S]2+, PLP, SAM, and L-alpha-lysine, a very close analog of the active Michaelis complex. The unit cell contains a dimer of hydrogen-bonded, domain-swapped dimers, the subunits of which adopt a fold that contains all three cofactors in a central channel defined by six beta/alpha structural units. Zinc coordination links the domain-swapped dimers. In each subunit, the solvent face of the channel is occluded by an N-terminal helical domain, with the opposite end of the channel packed against the domain-swapped subunit. Hydrogen-bonded ionic contacts hold the external aldimine of PLP and L-alpha-lysine in position for abstraction of the 3-pro-R hydrogen of lysine by C5' of SAM. The structure of the SAM/[4Fe-4S] complex confirms and extends conclusions from spectroscopic studies of LAM and shows selenium in Se-adenosyl-L-selenomethionine poised to ligate the unique iron in the [4Fe-4S] cluster upon electron transfer and radical formation. The chain fold in the central domain is in part analogous to other radical-SAM enzymes.
KeywordMeSH Terms
6. Song  KB, Frey  PA,     ( 1991 )

Molecular properties of lysine-2,3-aminomutase.

The Journal of biological chemistry 266 (12)
PMID : 2019591  :  
Abstract >>
Lysine-2,3-aminomutase purified from Clostridium subterminale SB4 is reported to exhibit an apparent subunit Mr of 48,000, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the undenatured enzyme exhibits an apparent Mr of 285,000, as determined by electrophoretic mobility and gel permeation chromatography (Chirpich, T. P., Zappia, V., Costilow, R. N., and Barker, H. A. (1970) J. Biol. Chem. 245, 1778-1789). The diffusion coefficient of the enzyme is 3.36 x 10(-7) cm2/s, as determined by quasielastic light scattering. The overall Mr calculated from the diffusion coefficient and the published sedimentation coefficient is 259,000. Cross-linking experiments using glutaraldehyde and dithiobis(succinimidylpropionate) as cross-linking reagents indicate that the enzyme has a hexameric quaternary structure. The number of major cyanogen bromide peptides, compared with the methionine content of the enzyme, is consistent with the subunits being identical, and isoelectric focusing also is consistent with identical subunits. The circular dichroism of the enzyme indicates that it is a highly ordered structure, which is estimated to consist of 26% alpha-helix and 48% beta-sheet. The enzyme contains approximately six molecules of pyridoxal 5'-phosphate per hexamer, as determined by the phenyl-hydrazine method. The amino acid analysis of the enzyme, after performic acid oxidation, indicates that it contains approximately 13 cysteine residues per subunit. Six sulfhydryl groups per hexamer react readily with 5,5'-dithiobis-2-nitrobenzoate, indicating that one sulfhydryl group is accessible per subunit.
KeywordMeSH Terms
Intramolecular Transferases
7. Petrovich  RM, Ruzicka  FJ, Reed  GH, Frey  PA,     ( 1991 )

Metal cofactors of lysine-2,3-aminomutase.

The Journal of biological chemistry 266 (12)
PMID : 1850415  :  
Abstract >>
Lysine-2,3-aminomutase from Clostridium SB4 contains iron and sulfide in equimolar amounts, as well as cobalt, zinc, and copper. The iron and sulfide apparently constitute an Fe-S cluster that is required as a cofactor of the enzyme. Although no B12 derivative can be detected, enzyme-bound cobalt is a cofactor; however, the zinc and copper bound to the enzyme do not appear to play a role in its catalytic activity. These conclusions are supported by the following facts reported in this paper. Purification of the enzyme under anaerobic conditions increases the iron and sulfide content. Lysine-2,3-aminomutase purified from cells grown in media supplemented with added CoCl2 contains higher levels of cobalt and correspondingly lower levels of zinc and copper relative to enzyme from cells grown in media not supplemented with cobalt. The specific activity of the purified enzyme increases with increasing iron and sulfide content, and it also increases with increasing cobalt and with decreasing zinc and copper content. The zinc and copper appear to occupy cobalt sites under conditions of insufficient cobalt in the growth medium, and they do not support the activity of the enzyme. The best preparations of lysine-2,3-aminomutase obtained to date exhibit a specific activity of approximately 23 units/mg of protein and contain about 12 g atoms of iron and of sulfide per mol of hexameric enzyme. These preparations also contain 3.5 g atoms of cobalt per mol, but even the best preparations contain small amounts of zinc and copper. The sum of cobalt, zinc, and copper in all preparations analyzed to date corresponds to 5.22 +/- 0.75 g atoms per mol of enzyme. An EPR spectrum of the enzyme as isolated reveals a signal corresponding to high spin Co(II) at temperatures below 20 K. The signal appears as a partially resolved 59Co octet centered at an apparent g value of 7. The 59Co hyperfine splitting (approximately 35 G) is prominent at 4.2 K. These findings show that lysine-2,3-aminomutase requires Fe-S clusters and cobalt as cofactors, in addition to the known requirement for pyridoxal 5'-phosphate and S-adenosylmethionine.
KeywordMeSH Terms
Intramolecular Transferases
8. Chirpich  TP, Zappia  V, Costilow  RN, Barker  HA,     ( 1970 )

Lysine 2,3-aminomutase. Purification and properties of a pyridoxal phosphate and S-adenosylmethionine-activated enzyme.

The Journal of biological chemistry 245 (7)
PMID : 5438361  :  
Abstract >>
KeywordMeSH Terms
Pyridoxal Phosphate

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