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L-lysine 2,3-aminomutase (LAM) (EC 5.4.3.2) (KAM)

 KAMA_CLOSU              Reviewed;         416 AA.
Q9XBQ8;
24-JAN-2006, integrated into UniProtKB/Swiss-Prot.
01-NOV-1999, sequence version 1.
12-SEP-2018, entry version 75.
RecName: Full=L-lysine 2,3-aminomutase;
Short=LAM;
EC=5.4.3.2;
AltName: Full=KAM;
Name=kamA;
Clostridium subterminale.
Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae;
Clostridium.
NCBI_TaxID=1550;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-16; 342-389
AND 401-416, AND CHARACTERIZATION.
STRAIN=SB4;
PubMed=10629195; DOI=10.1128/JB.182.2.469-476.2000;
Ruzicka F.J., Lieder K.W., Frey P.A.;
"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.";
J. Bacteriol. 182:469-476(2000).
[2]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
AND ACTIVITY REGULATION.
PubMed=5438361;
Chirpich T.P., Zappia V., Costilow R.N., Barker H.A.;
"Lysine 2,3-aminomutase. Purification and properties of a pyridoxal
phosphate and S-adenosylmethionine-activated enzyme.";
J. Biol. Chem. 245:1778-1789(1970).
[3]
SUBUNIT.
STRAIN=SB4;
PubMed=2019591;
Song K.B., Frey P.A.;
"Molecular properties of lysine-2,3-aminomutase.";
J. Biol. Chem. 266:7651-7655(1991).
[4]
FUNCTION, COFACTOR, AND ACTIVITY REGULATION.
PubMed=1850415;
Petrovich R.M., Ruzicka F.J., Reed G.H., Frey P.A.;
"Metal cofactors of lysine-2,3-aminomutase.";
J. Biol. Chem. 266:7656-7660(1991).
[5]
FUNCTION, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=1329954; DOI=10.1021/bi00159a019;
Petrovich R.M., Ruzicka F.J., Reed G.H., Frey P.A.;
"Characterization of iron-sulfur clusters in lysine 2,3-aminomutase by
electron paramagnetic resonance spectroscopy.";
Biochemistry 31:10774-10781(1992).
[6]
ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=11370852; DOI=10.1006/abbi.2001.2261;
Miller J., Bandarian V., Reed G.H., Frey P.A.;
"Inhibition of lysine 2,3-aminomutase by the alternative substrate 4-
thialysine and characterization of the 4-thialysyl radical
intermediate.";
Arch. Biochem. Biophys. 387:281-288(2001).
[7]
MUTAGENESIS OF GLU-86; ASP-96; ARG-130; ARG-134; ARG-135; ARG-136;
ASP-165; ASP-172; GLU-236; ASP-293 AND ASP-330.
PubMed=17042481; DOI=10.1021/bi061329l;
Chen D., Frey P.A., Lepore B.W., Ringe D., Ruzicka F.J.;
"Identification of structural and catalytic classes of highly
conserved amino acid residues in lysine 2,3-aminomutase.";
Biochemistry 45:12647-12653(2006).
[8]
X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND
COFACTOR.
STRAIN=SB4;
PubMed=16166264; DOI=10.1073/pnas.0505726102;
Lepore B.W., Ruzicka F.J., Frey P.A., Ringe D.;
"The X-ray crystal structure of lysine-2,3-aminomutase from
Clostridium subterminale.";
Proc. Natl. Acad. Sci. U.S.A. 102:13819-13824(2005).
-!- FUNCTION: Catalyzes the interconversion of L-alpha-lysine and L-
beta-lysine. {ECO:0000269|PubMed:1329954,
ECO:0000269|PubMed:1850415, ECO:0000269|PubMed:5438361}.
-!- CATALYTIC ACTIVITY: L-lysine = (3S)-3,6-diaminohexanoate.
{ECO:0000269|PubMed:5438361}.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Note=Binds 1 [4Fe-4S] cluster per subunit. The cluster is
coordinated with 3 cysteines and an exchangeable S-adenosyl-L-
methionine.;
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
-!- COFACTOR:
Name=Co(2+); Xref=ChEBI:CHEBI:48828;
Note=Binds 1 Co(2+) ion per subunit.;
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Note=Binds 1 zinc ion per subunit.;
-!- ACTIVITY REGULATION: The enzyme is activated by S-adenosyl-
methionine. Activity is dependent on the levels of Fe(2+), S(2-)
and Co(2+). Activity is stimulated by addition of EDTA. S-
adenosylhomocysteine competitively inhibits the activity whereas
5'-methylthioadenosine is not inhibitory in the presence of S-
adenosylmethionine. Competitively inhibited by 4-thialysine.
Inhibited by sodium borohydride (1 mM) when added with 2 mM
dithionate. Moderately inhibited by beta-mercaptoethanol (30 mM)
along with dithionate. Higher concentrations of Fe(2+) partially
inhibit the activity and Co(2+) at 1 mM is a strong inhibitor.
Hydroxylamine, isonicotinic acid hydrazide inhibit effectively, in
addition, hydrazine, D-penicillamine and D-cycloserine are also
inhibitory at high concentrations. {ECO:0000269|PubMed:11370852,
ECO:0000269|PubMed:1850415, ECO:0000269|PubMed:5438361}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=6.6 uM for L-lysine {ECO:0000269|PubMed:11370852,
ECO:0000269|PubMed:1329954, ECO:0000269|PubMed:5438361};
KM=28 nM for adenosylmethionine {ECO:0000269|PubMed:11370852,
ECO:0000269|PubMed:1329954, ECO:0000269|PubMed:5438361};
KM=1.4 mM for 4-thialysine {ECO:0000269|PubMed:11370852,
ECO:0000269|PubMed:1329954, ECO:0000269|PubMed:5438361};
Vmax=0.19 umol/min/mg enzyme with 4-thialysine as substrate (at
37 degrees Celsius and pH 8) {ECO:0000269|PubMed:11370852,
ECO:0000269|PubMed:1329954, ECO:0000269|PubMed:5438361};
pH dependence:
Optimum pH is 8.0. Displays half maximal activity between pH 6.0
and 9.8. {ECO:0000269|PubMed:11370852,
ECO:0000269|PubMed:1329954, ECO:0000269|PubMed:5438361};
Redox potential:
E(0) is between -336 and -370 mV for 4Fe-4S cluster.
{ECO:0000269|PubMed:11370852, ECO:0000269|PubMed:1329954,
ECO:0000269|PubMed:5438361};
Temperature dependence:
Optimum temperature is 37 degrees Celsius. It has strong
activity at 37 degrees Celsius but is reversibly inactivated in
temperatures between 37 and 65 degrees Celsius. Minimal loss of
activity is observed in enzyme stored at -10 degrees Celsius in
the presence of 15% glycerol. {ECO:0000269|PubMed:11370852,
ECO:0000269|PubMed:1329954, ECO:0000269|PubMed:5438361};
-!- PATHWAY: Amino-acid degradation; L-lysine degradation via acetate
pathway.
-!- SUBUNIT: Homohexamer; trimer of dimers. Forms a homotetramer in
crystal. {ECO:0000269|PubMed:16166264,
ECO:0000269|PubMed:2019591}.
-!- SIMILARITY: Belongs to the radical SAM superfamily. KamA family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AF159146; AAD43134.1; -; Genomic_DNA.
PDB; 2A5H; X-ray; 2.10 A; A/B/C/D=1-416.
PDBsum; 2A5H; -.
ProteinModelPortal; Q9XBQ8; -.
SMR; Q9XBQ8; -.
PRIDE; Q9XBQ8; -.
BioCyc; MetaCyc:MONOMER-12270; -.
BRENDA; 5.4.3.2; 1523.
UniPathway; UPA00870; -.
EvolutionaryTrace; Q9XBQ8; -.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0050066; F:lysine 2,3-aminomutase activity; IEA:UniProtKB-EC.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0019475; P:L-lysine catabolic process to acetate; IEA:UniProtKB-UniPathway.
Gene3D; 3.20.20.70; -; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR025895; LAM_C_dom.
InterPro; IPR003739; Lys_aminomutase/Glu_NH3_mut.
InterPro; IPR022459; Lysine_aminomutase.
InterPro; IPR007197; rSAM.
PANTHER; PTHR30538; PTHR30538; 1.
Pfam; PF12544; LAM_C; 1.
Pfam; PF04055; Radical_SAM; 1.
PIRSF; PIRSF004911; DUF160; 1.
SFLD; SFLDF00283; L-lysine_2_3-aminomutase_(LAM-; 1.
SFLD; SFLDG01070; PLP-dependent; 1.
SFLD; SFLDS00029; Radical_SAM; 1.
TIGRFAMs; TIGR03820; lys_2_3_AblA; 1.
TIGRFAMs; TIGR00238; TIGR00238; 1.
1: Evidence at protein level;
3D-structure; 4Fe-4S; Cobalt; Direct protein sequencing; Iron;
Iron-sulfur; Isomerase; Metal-binding; Pyridoxal phosphate;
S-adenosyl-L-methionine; Zinc.
CHAIN 1 416 L-lysine 2,3-aminomutase.
/FTId=PRO_0000172287.
METAL 125 125 Iron-sulfur (4Fe-4S-S-AdoMet).
METAL 129 129 Iron-sulfur (4Fe-4S-S-AdoMet).
METAL 132 132 Iron-sulfur (4Fe-4S-S-AdoMet).
METAL 268 268 Zinc.
METAL 375 375 Zinc.
METAL 377 377 Zinc.
METAL 380 380 Zinc.
MOD_RES 337 337 N6-(pyridoxal phosphate)lysine.
MUTAGEN 86 86 E->Q: Reduction in activity. Decrease in
iron and sulfide and PLP content.
{ECO:0000269|PubMed:17042481}.
MUTAGEN 96 96 D->N: Reduction in activity. Decrease in
iron and sulfide and PLP content.
{ECO:0000269|PubMed:17042481}.
MUTAGEN 130 130 R->Q,K: Complete loss of activity.
Decrease in iron and sulfide but not PLP
content. Destabilise the iron-sulfur
centers. {ECO:0000269|PubMed:17042481}.
MUTAGEN 134 134 R->K: Complete loss of activity.
Significant decrease in iron and sulfide
and PLP content.
{ECO:0000269|PubMed:17042481}.
MUTAGEN 134 134 R->Q: Complete loss of activity. Slight
decrease in iron and sulfide and PLP
content. {ECO:0000269|PubMed:17042481}.
MUTAGEN 135 135 R->K: Reduction in activity. Decrease in
iron and sulfide and PLP content.
{ECO:0000269|PubMed:17042481}.
MUTAGEN 135 135 R->Q: Reduction in activity. Significant
decrease in iron and sulfide and PLP
content. {ECO:0000269|PubMed:17042481}.
MUTAGEN 136 136 R->Q: Reduction in activity. Significant
decrease in iron and sulfide and PLP
content. {ECO:0000269|PubMed:17042481}.
MUTAGEN 165 165 D->N: Significant reduction in activity.
Decrease in iron and sulfide and PLP
content. {ECO:0000269|PubMed:17042481}.
MUTAGEN 172 172 D->N: Complete loss of activity. Decrease
in iron and sulfide and PLP content.
Destabilise the iron-sulfur centers.
{ECO:0000269|PubMed:17042481}.
MUTAGEN 236 236 E->Q: Significant reduction in activity.
Decrease in iron and sulfide and PLP
content. {ECO:0000269|PubMed:17042481}.
MUTAGEN 293 293 D->N: Complete loss of activity. Decrease
in iron and sulfide and PLP content.
{ECO:0000269|PubMed:17042481}.
MUTAGEN 330 330 D->A,N: Complete loss of activity.
Decrease in iron and sulfide and PLP
content. {ECO:0000269|PubMed:17042481}.
HELIX 4 8 {ECO:0000244|PDB:2A5H}.
HELIX 14 17 {ECO:0000244|PDB:2A5H}.
HELIX 20 25 {ECO:0000244|PDB:2A5H}.
HELIX 31 35 {ECO:0000244|PDB:2A5H}.
HELIX 42 49 {ECO:0000244|PDB:2A5H}.
HELIX 61 64 {ECO:0000244|PDB:2A5H}.
HELIX 75 80 {ECO:0000244|PDB:2A5H}.
HELIX 84 87 {ECO:0000244|PDB:2A5H}.
STRAND 94 96 {ECO:0000244|PDB:2A5H}.
TURN 100 102 {ECO:0000244|PDB:2A5H}.
STRAND 113 123 {ECO:0000244|PDB:2A5H}.
TURN 133 139 {ECO:0000244|PDB:2A5H}.
STRAND 140 144 {ECO:0000244|PDB:2A5H}.
HELIX 147 158 {ECO:0000244|PDB:2A5H}.
STRAND 165 171 {ECO:0000244|PDB:2A5H}.
HELIX 178 189 {ECO:0000244|PDB:2A5H}.
STRAND 196 200 {ECO:0000244|PDB:2A5H}.
HELIX 203 206 {ECO:0000244|PDB:2A5H}.
HELIX 208 210 {ECO:0000244|PDB:2A5H}.
HELIX 213 219 {ECO:0000244|PDB:2A5H}.
HELIX 220 222 {ECO:0000244|PDB:2A5H}.
STRAND 224 229 {ECO:0000244|PDB:2A5H}.
HELIX 234 236 {ECO:0000244|PDB:2A5H}.
HELIX 239 250 {ECO:0000244|PDB:2A5H}.
STRAND 255 260 {ECO:0000244|PDB:2A5H}.
TURN 263 265 {ECO:0000244|PDB:2A5H}.
HELIX 269 281 {ECO:0000244|PDB:2A5H}.
STRAND 284 290 {ECO:0000244|PDB:2A5H}.
HELIX 299 301 {ECO:0000244|PDB:2A5H}.
HELIX 305 313 {ECO:0000244|PDB:2A5H}.
HELIX 321 323 {ECO:0000244|PDB:2A5H}.
STRAND 326 331 {ECO:0000244|PDB:2A5H}.
TURN 332 335 {ECO:0000244|PDB:2A5H}.
STRAND 336 339 {ECO:0000244|PDB:2A5H}.
STRAND 345 349 {ECO:0000244|PDB:2A5H}.
STRAND 352 356 {ECO:0000244|PDB:2A5H}.
STRAND 362 366 {ECO:0000244|PDB:2A5H}.
TURN 378 382 {ECO:0000244|PDB:2A5H}.
HELIX 390 395 {ECO:0000244|PDB:2A5H}.
STRAND 400 402 {ECO:0000244|PDB:2A5H}.
HELIX 408 410 {ECO:0000244|PDB:2A5H}.
SEQUENCE 416 AA; 47102 MW; 6C3602E5B87E25A1 CRC64;
MINRRYELFK DVSDADWNDW RWQVRNRIET VEELKKYIPL TKEEEEGVAQ CVKSLRMAIT
PYYLSLIDPN DPNDPVRKQA IPTALELNKA AADLEDPLHE DTDSPVPGLT HRYPDRVLLL
ITDMCSMYCR HCTRRRFAGQ SDDSMPMERI DKAIDYIRNT PQVRDVLLSG GDALLVSDET
LEYIIAKLRE IPHVEIVRIG SRTPVVLPQR ITPELVNMLK KYHPVWLNTH FNHPNEITEE
STRACQLLAD AGVPLGNQSV LLRGVNDCVH VMKELVNKLV KIRVRPYYIY QCDLSLGLEH
FRTPVSKGIE IIEGLRGHTS GYCVPTFVVD APGGGGKTPV MPNYVISQSH DKVILRNFEG
VITTYSEPIN YTPGCNCDVC TGKKKVHKVG VAGLLNGEGM ALEPVGLERN KRHVQE


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