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 | N6-((3-Hydroxy-2-methyl-5-((phosphonooxy)methyl)-4-pyridinyl)methylene)-L-lysine | Ligand Info | |||
| Canonical SMILES | CC1=NC=C(C(=C1O)C=NCCCCC(C(=O)O)N)COP(=O)(O)O | ||||
| InChI | 1S/C14H22N3O7P/c1-9-13(18)11(10(6-17-9)8-24-25(21,22)23)7-16-5-3-2-4-12(15)14(19)20/h6-7,12,18H,2-5,8,15H2,1H3,(H,19,20)(H2,21,22,23)/t12-/m0/s1 | ||||
| InChIKey | YQSOQJORMNSDJL-LBPRGKRZSA-N | ||||
| PubChem Compound ID | 135412779 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 5X30 Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates. | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [1] |
| PDB Sequence |
> Chain A
LPGFATRAIH 16 HGYDPQDHGG26 ALVPPVYQTA36 TFTFPTVEYG46 AACFAGEQAG56 HFYSRISNPT 66 LNLLEARMAS76 LEGGEAGLAL86 ASGMGAITST96 LWTLLRPGDE106 VLLGNTLYGH 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 AQHPASMTHS357 SYTPEERAHY 367 GISEGLVRLS377 VGLEDIDDLL387 ADVQQALKAS397 A> Chain B 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
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SER88[A]
3.337
GLY89[A]
2.880
MET90[A]
2.805
GLY91[A]
4.895
ILE93[A]
3.769
TYR114[A]
3.403
THR117[A]
4.466
GLU157[A]
4.234
ASP186[A]
2.792
THR188[A]
3.694
TYR189[A]
3.843
SER208[A]
2.868
ALA209[A]
3.053
|
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| PDB ID: 3VK3 Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant Complexed with L-methionine | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | Yes | [2] |
| PDB Sequence |
HGSNKLPGFA
11 TRAIHHGYDP21 QDHGGALVPP31 VYQTATFTFP41 TVEYGAACFA51 GEQAGHFYSR 61 ISNPTLNLLE71 ARMASLEGGE81 AGLALASGMG91 AITSTLWTLL101 RPGDEVLLGN 111 TLYGHTFAFL121 HHGIGEFGVK131 LRHVDMADLQ141 ALEAAMTPAT151 RVIYFESPAN 161 PNMHMADIAG171 VAKIARKHGA181 TVVVDNTYCT191 PYLQRPLELG201 ADLVVHSATY 212 LSGHGDITAG222 IVVGSQALVD232 RIRLQGLKDM242 TGAVLSPHDA252 ALLMRGIKTL 262 NLRMDRHCAN272 AQVLAEFLAR282 QPQVELIHYP292 GLASFPQYTL302 ARQQMSQPGG 312 MIAFELKGGI322 GAGRRFMNAL332 QLFSRAVSLG342 DAESLAQHPA352 SMTHSSYTPE 362 ERAHYGISEG372 LVRLSVGLED382 IDDLLADVQQ392 ALKASA
|
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|
|
SER88
3.390
GLY89
2.879
MET90
2.918
ILE93
3.735
TYR114
3.471
THR117
4.588
GLU157
4.414
ASP186
2.743
THR188
3.697
TYR189
3.885
SER208
2.819
ALA209
2.958
|
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| PDB ID: 7F1V Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-homocysteine intermediates | ||||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | Yes | [3] |
| 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
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|
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TYR59[A]
2.508
ARG61[A]
2.801
SER88[B]
3.467
GLY89[B]
3.001
MET90[B]
2.878
GLY91[B]
4.940
ILE93[B]
3.799
TYR114[B]
3.506
THR117[B]
4.472
GLU157[B]
4.328
ASP186[B]
2.827
THR188[B]
3.769
TYR189[B]
4.003
|
|||||
| 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 | [3] |
| 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
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LLP or .LLP2 or .LLP3 or :3LLP;style chemicals stick;color identity;select .A:59 or .A:61 or .B:88 or .B:89 or .B:90 or .B:91 or .B:93 or .B:114 or .B:117 or .B:157 or .B:161 or .B:186 or .B:188 or .B:189 or .B:208 or .B:209 or .B:210 or .B:212 or .B:213 or .B:214 or .B:215 or .B:216 or .B:220 or .B:221 or .B:340 or .B:341 or .B:342; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
TYR59[A]
2.564
ARG61[A]
2.707
SER88[B]
3.413
GLY89[B]
2.935
MET90[B]
2.813
GLY91[B]
4.892
ILE93[B]
3.924
TYR114[B]
3.558
THR117[B]
4.624
GLU157[B]
4.396
ASN161[B]
3.876
ASP186[B]
2.769
THR188[B]
3.704
TYR189[B]
4.005
|
|||||
| PDB ID: 3VK4 Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant complexed with L-homocysteine | ||||||
| Method | X-ray diffraction | Resolution | 2.61 Å | Mutation | Yes | [2] |
| 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 HSATYLSGHG 217 DITAGIVVGS227 QALVDRIRLQ237 GLKDMTGAVL247 SPHDAALLMR257 GIKTLNLRMD 267 RHCANAQVLA277 EFLARQPQVE287 LIHYPGLASF297 PQYTLARQQM307 SQPGGMIAFE 317 LKGGIGAGRR327 FMNALQLFSR337 AVSLGDAESL347 AQHPASMTHS357 SYTPEERAHY 367 GISEGLVRLS377 VGLEDIDDLL387 ADVQQALKAS397 A
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LLP or .LLP2 or .LLP3 or :3LLP;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:114 or .A:117 or .A:157 or .A:186 or .A:188 or .A:189 or .A:208 or .A:209 or .A:210 or .A:212 or .A:213 or .A:214 or .A:215 or .A:216 or .A:220 or .A:221 or .A:340 or .A:341 or .A:342 or .A:343; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER88
3.632
GLY89
2.575
MET90
2.774
GLY91
4.899
TYR114
3.312
THR117
4.655
GLU157
4.533
ASP186
2.703
THR188
3.715
TYR189
3.865
SER208
2.880
ALA209
2.924
|
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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 | The role of amino acid residues in the active site of L-methionine Gamma-lyase from Pseudomonas putida. Biosci Biotechnol Biochem. 2012;76(7):1275-84. | ||||
| REF 3 | 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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