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L-methionine gamma-lyase (MGL) (EC 4.4.1.11) (Homocysteine desulfhydrase) (EC 4.4.1.2) (L-methioninase)

 MEGL_PSEPU              Reviewed;         398 AA.
P13254;
01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
01-OCT-1996, sequence version 2.
28-FEB-2018, entry version 103.
RecName: Full=L-methionine gamma-lyase {ECO:0000303|PubMed:6742420, ECO:0000303|PubMed:8586629};
Short=MGL {ECO:0000303|PubMed:10965031};
EC=4.4.1.11 {ECO:0000269|PubMed:22785484, ECO:0000269|PubMed:6742420};
AltName: Full=Homocysteine desulfhydrase {ECO:0000305|PubMed:6742420};
EC=4.4.1.2 {ECO:0000269|PubMed:22785484, ECO:0000269|PubMed:6742420};
AltName: Full=L-methioninase;
Name=mdeA {ECO:0000312|EMBL:BAA20553.1};
Pseudomonas putida (Arthrobacter siderocapsulatus).
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
Pseudomonadaceae; Pseudomonas.
NCBI_TaxID=303;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
STRAIN=ICR 3460;
PubMed=8586629;
Inoue H., Sugimoto M., Inagaki K., Esaki N., Soda K., Tanaka H.;
"Structural analysis of the L-methionine gamma-lyase gene from
Pseudomonas putida.";
J. Biochem. 117:1120-1125(1995).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND INDUCTION.
STRAIN=ICR 3460;
PubMed=9190812; DOI=10.1128/jb.179.12.3956-3962.1997;
Inoue H., Inagaki K., Eriguchi S.I., Tamura T., Esaki N., Soda K.,
Tanaka H.;
"Molecular characterization of the mde operon involved in L-methionine
catabolism of Pseudomonas putida.";
J. Bacteriol. 179:3956-3962(1997).
[3]
PROTEIN SEQUENCE OF 91-137 AND 167-213, AND PYRIDOXAL PHOSPHATE AT
LYS-211.
STRAIN=ICR 3460;
PubMed=3365412; DOI=10.1021/bi00405a029;
Nakayama T., Esaki N., Tanaka H., Soda K.;
"Specific labeling of the essential cysteine residue of L-methionine
gamma-lyase with a cofactor analogue, N-(bromoacetyl)pyridoxamine
phosphate.";
Biochemistry 27:1587-1591(1988).
[4]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBSTRATE SPECIFICITY,
BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
STRAIN=ICR 3460;
PubMed=6742420; DOI=10.1016/0003-2697(84)90832-7;
Nakayama T., Esaki N., Sugie K., Beresov T.T., Tanaka H., Soda K.;
"Purification of bacterial L-methionine gamma-lyase.";
Anal. Biochem. 138:421-424(1984).
[5]
REVIEW, AND BIOTECHNOLOGY.
PubMed=25439528; DOI=10.1517/14712598.2015.963050;
Hoffman R.M.;
"Development of recombinant methioninase to target the general cancer-
specific metabolic defect of methionine dependence: a 40-year
odyssey.";
Expert Opin. Biol. Ther. 15:21-31(2015).
[6]
X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS).
PubMed=10965031; DOI=10.1093/oxfordjournals.jbchem.a022760;
Motoshima H., Inagaki K., Kumasaka T., Furuichi M., Inoue H.,
Tamura T., Esaki N., Soda K., Tanaka N., Yamamoto M., Tanaka H.;
"Crystal structure of the pyridoxal 5'-phosphate dependent L-
methionine gamma-lyase from Pseudomonas putida.";
J. Biochem. 128:349-354(2000).
[7]
X-RAY CRYSTALLOGRAPHY (2.68 ANGSTROMS) IN COVALENT COMPLEX WITH PLP.
Allen T.W., Sridhar V., Prasad G.S., Han Q., Xu M., Tan Y.,
Hoffman R.M., Ramaswamy S.;
"Crystal structure of L-methionine alpha-, gamma-lyase.";
Submitted (MAY-2003) to the PDB data bank.
[8]
X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COVALENT COMPLEX WITH PLP.
Misaki S., Takimoto A., Takakura T., Yoshioka T., Yamashita M.,
Tamura T., Tanaka H., Inagaki K.;
"Detailed structure of L-methionine-lyase from Pseudomonas putida.";
Submitted (AUG-2003) to the PDB data bank.
[9]
X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COVALENT COMPLEX WITH PLP,
COFACTOR, SUBUNIT, AND MUTAGENESIS OF ARG-61 AND CYS-116.
STRAIN=ICR 3460;
PubMed=17289792; DOI=10.1093/jb/mvm055;
Kudou D., Misaki S., Yamashita M., Tamura T., Takakura T.,
Yoshioka T., Yagi S., Hoffman R.M., Takimoto A., Esaki N., Inagaki K.;
"Structure of the antitumour enzyme L-methionine gamma-lyase from
Pseudomonas putida at 1.8 A resolution.";
J. Biochem. 141:535-544(2007).
[10]
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF MUTANT HIS-116 IN COMPLEXES
WITH L-HOMOCYSTEINE; METHIONINE AND PLP, FUNCTION, CATALYTIC ACTIVITY,
BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, ENZYME REGULATION, AND
MUTAGENESIS OF CYS-116; LYS-240 AND ASP-241.
PubMed=22785484; DOI=10.1271/bbb.110906;
Fukumoto M., Kudou D., Murano S., Shiba T., Sato D., Tamura T.,
Harada S., Inagaki K.;
"The role of amino acid residues in the active site of L-methionine
gamma-lyase from Pseudomonas putida.";
Biosci. Biotechnol. Biochem. 76:1275-1284(2012).
-!- FUNCTION: Catalyzes the alpha,gamma-elimination of L-methionine to
produce methanethiol, 2-oxobutanoate and ammonia (PubMed:8586629,
PubMed:6742420). Is involved in L-methionine catabolism
(PubMed:9190812). In fact, shows a multicatalytic function since
it also catalyzes gamma-replacement of L-methionine with thiol
compounds, alpha,gamma-elimination and gamma-replacement reactions
of L-homocysteine and its S-substituted derivatives, O-
substituted-L-homoserines and DL-selenomethionine, and, to a
lesser extent, alpha,beta-elimination and beta-replacement
reactions of L-cysteine, S-methyl-L-cysteine, and O-acetyl-L-
serine (PubMed:6742420, PubMed:22785484). Also catalyzes
deamination and gamma-addition reactions of L-vinylglycine
(PubMed:6742420). Thus, the enzyme is able to cleave C-S, C-Se,
and C-O bonds of sulfur, selenium, and oxygen amino acids,
respectively (PubMed:6742420, PubMed:22785484).
{ECO:0000269|PubMed:22785484, ECO:0000269|PubMed:6742420,
ECO:0000269|PubMed:8586629, ECO:0000305|PubMed:9190812}.
-!- CATALYTIC ACTIVITY: L-methionine + H(2)O = methanethiol + NH(3) +
2-oxobutanoate. {ECO:0000269|PubMed:22785484,
ECO:0000269|PubMed:6742420}.
-!- CATALYTIC ACTIVITY: L-homocysteine + H(2)O = H(2)S + NH(3) + 2-
oxobutanoate. {ECO:0000269|PubMed:22785484,
ECO:0000269|PubMed:6742420}.
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
Evidence={ECO:0000269|PubMed:17289792,
ECO:0000269|PubMed:22785484, ECO:0000269|PubMed:6742420};
-!- ENZYME REGULATION: Irreversibly inactivated by DL-
propargylglycine. {ECO:0000269|PubMed:22785484}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1.0 mM for L-methionine {ECO:0000269|PubMed:6742420};
KM=0.5 mM for L-methionine {ECO:0000269|PubMed:22785484};
KM=1.1 mM for DL-homocysteine {ECO:0000269|PubMed:22785484};
KM=0.2 mM for L-cysteine {ECO:0000269|PubMed:22785484};
KM=0.7 mM for S-methyl-L-cysteine {ECO:0000269|PubMed:22785484};
KM=7.2 mM for O-succinyl-L-homoserine
{ECO:0000269|PubMed:22785484};
Note=kcat is 33.4 sec(-1) for the alpha,gamma-elimination of L-
methionine. kcat is 71.0 sec(-1) for the alpha,gamma-elimination
of DL-homocysteine. kcat is 2.13 sec(-1) for the alpha,beta-
elimination of L-cysteine. kcat is 1.58 sec(-1) for the
alpha,beta-elimination of S-methyl-L-cysteine. kcat is 2.56
sec(-1) for the alpha,gamma-elimination of O-succinyl-L-
homoserine. {ECO:0000269|PubMed:22785484};
-!- SUBUNIT: Homotetramer; dimer of active dimers.
{ECO:0000269|PubMed:17289792, ECO:0000269|PubMed:6742420}.
-!- INDUCTION: Is under the control of the positive transcriptional
regulator MdeR. Forms part of an operon with mdeB.
{ECO:0000269|PubMed:9190812}.
-!- BIOTECHNOLOGY: The recombinant MGL protein cloned form P.putida
has been found to have antitumor efficacy in vitro and in vivo.
PEGylated MGL is being developed as a cancer drug.
{ECO:0000303|PubMed:25439528}.
-!- SIMILARITY: Belongs to the trans-sulfuration enzymes family. L-
methionine gamma-lyase subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; D88554; BAA13642.1; -; Genomic_DNA.
EMBL; D89015; BAA20553.1; -; Genomic_DNA.
PIR; A27691; A27691.
PIR; JC4174; JC4174.
PDB; 1GC0; X-ray; 1.70 A; A/B/C/D=1-398.
PDB; 1GC2; X-ray; 2.00 A; A/B/C/D=1-398.
PDB; 1PG8; X-ray; 2.68 A; A/B/C/D=1-398.
PDB; 1UKJ; X-ray; 1.80 A; A/B/C/D=1-398.
PDB; 2O7C; X-ray; 1.70 A; A/B/C/D=1-398.
PDB; 3VK2; X-ray; 2.30 A; A/B/C/D=1-398.
PDB; 3VK3; X-ray; 2.10 A; A/B/C/D=1-398.
PDB; 3VK4; X-ray; 2.61 A; A/B/C/D=1-398.
PDB; 5X2V; X-ray; 2.40 A; A/B/C/D=1-398.
PDB; 5X2W; X-ray; 2.70 A; A/B/C/D=1-398.
PDB; 5X2X; X-ray; 2.00 A; A/B/C/D=1-398.
PDB; 5X2Y; X-ray; 1.79 A; A/B/C/D=1-398.
PDB; 5X2Z; X-ray; 1.80 A; A/B/C/D=1-398.
PDB; 5X30; X-ray; 1.70 A; A/B/C/D=1-398.
PDBsum; 1GC0; -.
PDBsum; 1GC2; -.
PDBsum; 1PG8; -.
PDBsum; 1UKJ; -.
PDBsum; 2O7C; -.
PDBsum; 3VK2; -.
PDBsum; 3VK3; -.
PDBsum; 3VK4; -.
PDBsum; 5X2V; -.
PDBsum; 5X2W; -.
PDBsum; 5X2X; -.
PDBsum; 5X2Y; -.
PDBsum; 5X2Z; -.
PDBsum; 5X30; -.
ProteinModelPortal; P13254; -.
SMR; P13254; -.
DrugBank; DB04083; N'-Pyridoxyl-Lysine-5'-Monophosphate.
BioCyc; MetaCyc:MONOMER-284; -.
BRENDA; 4.4.1.11; 5092.
EvolutionaryTrace; P13254; -.
GO; GO:0047982; F:homocysteine desulfhydrase activity; IEA:UniProtKB-EC.
GO; GO:0018826; F:methionine gamma-lyase activity; IEA:UniProtKB-EC.
GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
CDD; cd00614; CGS_like; 1.
Gene3D; 3.40.640.10; -; 1.
Gene3D; 3.90.1150.10; -; 1.
InterPro; IPR000277; Cys/Met-Metab_PyrdxlP-dep_enz.
InterPro; IPR006237; L-Met_gamma_lys.
InterPro; IPR015424; PyrdxlP-dep_Trfase.
InterPro; IPR015422; PyrdxlP-dep_Trfase_dom1.
InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
PANTHER; PTHR11808; PTHR11808; 1.
Pfam; PF01053; Cys_Met_Meta_PP; 1.
PIRSF; PIRSF001434; CGS; 1.
SUPFAM; SSF53383; SSF53383; 1.
TIGRFAMs; TIGR01328; met_gam_lyase; 1.
PROSITE; PS00868; CYS_MET_METAB_PP; 1.
1: Evidence at protein level;
3D-structure; Direct protein sequencing; Lyase; Pyridoxal phosphate.
CHAIN 1 398 L-methionine gamma-lyase.
/FTId=PRO_0000114784.
REGION 59 61 Pyridoxal phosphate binding; shared with
dimeric partner. {ECO:0000269|Ref.7}.
REGION 89 90 Pyridoxal phosphate binding.
{ECO:0000269|Ref.7}.
REGION 208 210 Pyridoxal phosphate binding.
{ECO:0000269|Ref.7}.
BINDING 114 114 Substrate. {ECO:0000244|PDB:3VK3,
ECO:0000244|PDB:3VK4,
ECO:0000269|PubMed:22785484}.
BINDING 375 375 Substrate. {ECO:0000244|PDB:3VK3,
ECO:0000244|PDB:3VK4,
ECO:0000269|PubMed:22785484}.
MOD_RES 211 211 N6-(pyridoxal phosphate)lysine.
{ECO:0000244|PDB:1UKJ,
ECO:0000269|PubMed:17289792,
ECO:0000269|PubMed:22785484,
ECO:0000269|PubMed:3365412,
ECO:0000269|Ref.7, ECO:0000269|Ref.8}.
MUTAGEN 61 61 R->A,E,F: Loss of elimination activity
against L-methionine.
{ECO:0000269|PubMed:17289792}.
MUTAGEN 116 116 C->H: Drastic decrease of the catalytic
efficiency of the elimination reaction
with L-methionine, by 6700-fold, and
increases that with L-cysteine by 7-fold,
mainly due to changes in kcat. Loss of
ability to catalyze replacement reaction
between L-methionine and 2-
mercaptoethanol.
{ECO:0000269|PubMed:22785484}.
MUTAGEN 116 116 C->S: 9% of wild-type elimination
activity against L-methionine.
{ECO:0000269|PubMed:17289792}.
MUTAGEN 116 116 C->T: 40% of wild-type elimination
activity against L-methionine.
{ECO:0000269|PubMed:17289792}.
MUTAGEN 240 240 K->D,E: Marked decrease in elimination
activity against both L-methionine and
DL-homocysteine.
{ECO:0000269|PubMed:22785484}.
MUTAGEN 240 240 K->M: 50% reduction in alpha,gamma-
elimination activity against DL-
homocysteine, while retaining elimination
activity against L-methionine and L-
cysteine. {ECO:0000269|PubMed:22785484}.
MUTAGEN 241 241 D->H,R: 5 to 14-fold reduction in
alpha,gamma-elimination activity against
L-methionine, while no change in affinity
for L-methionine.
{ECO:0000269|PubMed:22785484}.
STRAND 3 7 {ECO:0000244|PDB:2O7C}.
HELIX 10 16 {ECO:0000244|PDB:1GC0}.
HELIX 21 24 {ECO:0000244|PDB:1GC0}.
STRAND 27 29 {ECO:0000244|PDB:1GC0}.
STRAND 36 38 {ECO:0000244|PDB:2O7C}.
STRAND 40 42 {ECO:0000244|PDB:5X30}.
HELIX 43 50 {ECO:0000244|PDB:2O7C}.
STRAND 54 56 {ECO:0000244|PDB:5X2X}.
TURN 60 62 {ECO:0000244|PDB:2O7C}.
HELIX 65 78 {ECO:0000244|PDB:1GC0}.
STRAND 81 88 {ECO:0000244|PDB:1GC0}.
HELIX 89 100 {ECO:0000244|PDB:1GC0}.
STRAND 106 112 {ECO:0000244|PDB:1GC0}.
HELIX 116 123 {ECO:0000244|PDB:1GC0}.
HELIX 125 128 {ECO:0000244|PDB:1GC0}.
STRAND 131 135 {ECO:0000244|PDB:1GC0}.
HELIX 140 146 {ECO:0000244|PDB:1GC0}.
STRAND 151 159 {ECO:0000244|PDB:1GC0}.
TURN 161 163 {ECO:0000244|PDB:1GC0}.
HELIX 169 176 {ECO:0000244|PDB:1GC0}.
HELIX 177 179 {ECO:0000244|PDB:1GC0}.
STRAND 182 186 {ECO:0000244|PDB:1GC0}.
TURN 188 190 {ECO:0000244|PDB:1GC0}.
HELIX 191 194 {ECO:0000244|PDB:1GC0}.
HELIX 197 200 {ECO:0000244|PDB:1GC0}.
STRAND 203 208 {ECO:0000244|PDB:1GC0}.
TURN 209 214 {ECO:0000244|PDB:5X30}.
STRAND 216 218 {ECO:0000244|PDB:1GC0}.
STRAND 222 226 {ECO:0000244|PDB:1GC0}.
HELIX 228 236 {ECO:0000244|PDB:1GC0}.
HELIX 238 242 {ECO:0000244|PDB:1GC0}.
HELIX 249 259 {ECO:0000244|PDB:1GC0}.
HELIX 262 281 {ECO:0000244|PDB:1GC0}.
STRAND 286 291 {ECO:0000244|PDB:1GC0}.
HELIX 300 306 {ECO:0000244|PDB:2O7C}.
STRAND 313 318 {ECO:0000244|PDB:1GC0}.
HELIX 321 331 {ECO:0000244|PDB:1GC0}.
STRAND 333 337 {ECO:0000244|PDB:1GC0}.
STRAND 343 345 {ECO:0000244|PDB:2O7C}.
STRAND 347 349 {ECO:0000244|PDB:1GC0}.
HELIX 351 353 {ECO:0000244|PDB:1GC0}.
TURN 354 356 {ECO:0000244|PDB:1GC0}.
STRAND 357 359 {ECO:0000244|PDB:1GC0}.
HELIX 361 366 {ECO:0000244|PDB:1GC0}.
STRAND 373 377 {ECO:0000244|PDB:1GC0}.
HELIX 383 397 {ECO:0000244|PDB:1GC0}.
SEQUENCE 398 AA; 42627 MW; BD50CD1F34CD71E3 CRC64;
MHGSNKLPGF ATRAIHHGYD PQDHGGALVP PVYQTATFTF PTVEYGAACF AGEQAGHFYS
RISNPTLNLL EARMASLEGG EAGLALASGM GAITSTLWTL LRPGDEVLLG NTLYGCTFAF
LHHGIGEFGV KLRHVDMADL QALEAAMTPA TRVIYFESPA NPNMHMADIA GVAKIARKHG
ATVVVDNTYC TPYLQRPLEL GADLVVHSAT KYLSGHGDIT AGIVVGSQAL VDRIRLQGLK
DMTGAVLSPH DAALLMRGIK TLNLRMDRHC ANAQVLAEFL ARQPQVELIH YPGLASFPQY
TLARQQMSQP GGMIAFELKG GIGAGRRFMN ALQLFSRAVS LGDAESLAQH PASMTHSSYT
PEERAHYGIS EGLVRLSVGL EDIDDLLADV QQALKASA


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