Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T06397 | Target Info | |||
| Target Name | Pseudomonas Methionine gamma-lyase (Pseudo mdeA) | ||||
| Synonyms | Pseudo MGL; L-methionine gamma-lyase; L-methioninase; Homocysteine desulfhydrase | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | Pseudo mdeA | ||||
| Biochemical Class | Carbon-sulfur lyases | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | (2e)-2-[({3-Hydroxy-2-Methyl-5-[(Phosphonooxy)methyl]pyridin-4-Yl}methyl)amino]-4-(Methylsulfanyl)but-2-Enoic Acid | Ligand Info | |||
| Canonical SMILES | CC1=NC=C(C(=C1O)CNC(=CCSC)C(=O)O)COP(=O)(O)O | ||||
| InChI | 1S/C13H19N2O7PS/c1-8-12(16)10(6-15-11(13(17)18)3-4-24-2)9(5-14-8)7-22-23(19,20)21/h3,5,15-16H,4,6-7H2,1-2H3,(H,17,18)(H2,19,20,21)/b11-3+ | ||||
| InChIKey | LPFNPHQQDYAHKU-QDEBKDIKSA-N | ||||
| PubChem Compound ID | 49852668 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 5X2Z Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-methionine intermediates | ||||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [1] |
| PDB Sequence |
LPGFATRAIH
16 HGYDPQDHGG26 ALVPPVYQTA36 TFTFPTVEYG46 AACFAGEQAG56 HFYSRISNPT 66 LNLLEARMAS76 LEGGEAGLAL86 ASGMGAITST96 LWTLLRPGDE106 VLLGNTLYGH 116 TFAFLHHGIG126 EFGVKLRHVD136 MADLQALEAA146 MTPATRVIYF156 ESPANPNMHM 166 ADIAGVAKIA176 RKHGATVVVD186 NTYCTPYLQR196 PLELGADLVV206 HSATKYLSGH 216 GDITAGIVVG226 SQALVDRIRL236 QGLKDMTGAV246 LSPHDAALLM256 RGIKTLNLRM 266 DRHCANAQVL276 AEFLARQPQV286 ELIHYPGLAS296 FPQYTLARQQ306 MSQPGGMIAF 316 ELKGGIGAGR326 RFMNALQLFS336 RAVSLGDAES346 LAQHPASMTH356 SSYTPEERAH 366 YGISEGLVRL376 SVGLEDIDDL386 LADVQQALKA396 SA
|
|||||
|
|
SER88
3.393
GLY89
2.823
MET90
2.844
GLY91
4.934
ILE93
3.776
TYR114
2.957
HIS116
4.181
THR117
4.610
GLU157
4.187
ASN161
4.457
ASP186
2.646
THR188
3.740
|
|||||
| PDB ID: 7F1U Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-methionine intermediates | ||||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | Yes | [2] |
| PDB Sequence |
> Chain A
GSNKLPGFAT 12 RAIHHGYDPQ22 DHGGALVPPV32 YQTATFTFPT42 VEYGAACFAG52 EQAGHFYSRI 62 SNPTLNLLEA72 RMASLEGGEA82 GLALASGMGA92 ITSTLWTLLR102 PGDEVLLGNT 112 LYGCTFAFLH122 HGIGEFGVKL132 RHVDMADLQA142 LEAAMTPATR152 VIYFESPANP 162 NMHMADIAGV172 AKIARKHGAT182 VVVDNTYCTP192 YLQRPLELGA202 DLVVHSATKY 212 LSGHGDITAG222 IVVGSQALVD232 RIRLQGLKDM242 TGAVLSPHDA252 ALLMRGIKTL 262 NLRMDRHCAN272 AQVLAEFLAR282 QPQVELIHYP292 GLASFPQYTL302 ARQQMSQPGG 312 MIAFELKGGI322 GAGRRFMNAL332 QLFSRAVSLG342 DAESLASHPA352 SMTHSSYTPE 362 ERAHYGISEG372 LVRLSVGLED382 IDDLLADVQQ392 ALKASA> Chain B LPGFATRAIH 16 HGYDPQDHGG26 ALVPPVYQTA36 TFTFPTVEYG46 AACFAGEQAG56 HFYSRISNPT 66 LNLLEARMAS76 LEGGEAGLAL86 ASGMGAITST96 LWTLLRPGDE106 VLLGNTLYGC 116 TFAFLHHGIG126 EFGVKLRHVD136 MADLQALEAA146 MTPATRVIYF156 ESPANPNMHM 166 ADIAGVAKIA176 RKHGATVVVD186 NTYCTPYLQR196 PLELGADLVV206 HSATYLSGHG 217 DITAGIVVGS227 QALVDRIRLQ237 GLKDMTGAVL247 SPHDAALLMR257 GIKTLNLRMD 267 RHCANAQVLA277 EFLARQPQVE287 LIHYPGLASF297 PQYTLARQQM307 SQPGGMIAFE 317 LKGGIGAGRR327 FMNALQLFSR337 AVSLGDAESL347 ASHPASMTHS357 SYTPEERAHY 367 GISEGLVRLS377 VGLEDIDDLL387 ADVQQALKAS397 A
|
|||||
|
|
SER88[A]
3.448
GLY89[A]
2.710
MET90[A]
2.777
GLY91[A]
4.969
ILE93[A]
3.761
TYR114[A]
3.108
CYS116[A]
4.704
THR117[A]
4.587
GLU157[A]
4.126
ASN161[A]
2.994
ASP186[A]
2.768
THR188[A]
3.742
TYR189[A]
4.249
SER208[A]
2.686
|
|||||
| PDB ID: 5X2W Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-methionine intermediates | ||||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [1] |
| PDB Sequence |
LPGFATRAIH
16 HGYDPQDHGG26 ALVPPVYQTA36 TFTFPTVEYG46 AACFAGEQAG56 HFYSRISNPT 66 LNLLEARMAS76 LEGGEAGLAL86 ASGMGAITST96 LWTLLRPGDE106 VLLGNTLYGC 116 TFAFLHHGIG126 EFGVKLRHVD136 MADLQALEAA146 MTPATRVIYF156 ESPANPNMHM 166 ADIAGVAKIA176 RKHGATVVVD186 NTYCTPYLQR196 PLELGADLVV206 HSATKYLSGH 216 GDITAGIVVG226 SQALVDRIRL236 QGLKDMTGAV246 LSPHDAALLM256 RGIKTLNLRM 266 DRHCANAQVL276 AEFLARQPQV286 ELIHYPGLAS296 FPQYTLARQQ306 MSQPGGMIAF 316 ELKGGIGAGR326 RFMNALQLFS336 RAVSLGDAES346 LAQHPASMTH356 SSYTPEERAH 366 YGISEGLVRL376 SVGLEDIDDL386 LADVQQALKA396 SA
|
|||||
|
|
SER88
3.374
GLY89
2.840
MET90
2.773
GLY91
4.849
ILE93
3.883
TYR114
2.971
CYS116
4.001
THR117
4.654
GLU157
4.414
ASN161
4.040
ASP186
2.919
THR188
3.822
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural and mechanistic insights into homocysteine degradation by a mutant of methionine Gamma-lyase based on substrate-assisted catalysis. Protein Sci. 2017 Jun;26(6):1224-1230. | ||||
| REF 2 | Characterization and application of l-methionine Gamma-lyase Q349S mutant enzyme with an enhanced activity toward l-homocysteine. J Biosci Bioeng. 2022 Mar;133(3):213-221. | ||||
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