Binding Site Information of Target
| 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 | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Pyridoxal phosphate | Ligand Info | |||||
| Structure Description | Crystal Structure of L-methionine alpha-, gamma-lyase | PDB:1PG8 | ||||
| Method | X-ray diffraction | Resolution | 2.68 Å | Mutation | No | [1] |
| PDB Sequence |
MHGSNKLPGF
10 ATRAIHHGYD20 PQDHGGALVP30 PVYQTATFTF40 PTVEYGAACF50 AGEQAGHFYS 60 RISNPTLNLL70 EARMASLEGG80 EAGLALASGM90 GAITSTLWTL100 LRPGDEVLLG 110 NTLYGCTFAF120 LHHGIGEFGV130 KLRHVDMADL140 QALEAAMTPA150 TRVIYFESPA 160 NPNMHMADIA170 GVAKIARKHG180 ATVVVDNTYC190 TPYLQRPLEL200 GADLVVHSAT 210 KYLSGHGDIT220 AGIVVGSQAL230 VDRIRLQGLK240 DMTGAVLSPH250 DAALLMRGIK 260 TLNLRMDRHC270 ANAQVLAEFL280 ARQPQVELIH290 YPGLASFPQY300 TLARQQMSQP 310 GGMIAFELKG320 GIGAGRRFMN330 ALQLFSRAVS340 LGDAESLAQH350 PASMTHSSYT 360 PEERAHYGIS370 EGLVRLSVGL380 EDIDDLLADV390 QQALKASA
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| Ligand Name: L-homocysteine | Ligand Info | |||||
| Structure Description | Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates. | PDB:5X30 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [2] |
| 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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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: L-methionine | Ligand Info | |||||
| Structure Description | Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant Complexed with L-methionine | PDB:3VK3 | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | Yes | [3] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MET or .MET2 or .MET3 or :3MET;style chemicals stick;color identity;select .A:114 or .A:116 or .A:161 or .A:189 or .A:339 or .A:340 or .A:341 or .A:349 or .A:375; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Hydrogen Sulfide | Ligand Info | |||||
| Structure Description | Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates. | PDB:5X30 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [2] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .H2S or .H2S2 or .H2S3 or :3H2S;style chemicals stick;color identity;select .A:50 or .B:114 or .B:116 or .B:339 or .B:355; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: N6-((3-Hydroxy-2-methyl-5-((phosphonooxy)methyl)-4-pyridinyl)methylene)-L-lysine | Ligand Info | |||||
| Structure Description | Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates. | PDB:5X30 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [2] |
| 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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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:93 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 .B:59 or .B:61; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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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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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (2e)-2-[({3-Hydroxy-2-Methyl-5-[(Phosphonooxy)methyl]pyridin-4-Yl}methyl)amino]-4-(Methylsulfanyl)but-2-Enoic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-methionine intermediates | PDB:5X2Z | ||||
| Method | X-ray diffraction | Resolution | 1.80 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 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3LM or .3LM2 or .3LM3 or :33LM;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:93 or .A:114 or .A:116 or .A:117 or .A:157 or .A:161 or .A:186 or .A:188 or .A:189 or .A:208 or .A:210 or .A:211 or .A:220 or .A:221 or .A:339 or .A:340 or .A:341 or .A:349 or .A:355 or .A:375; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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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
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (2~{s})-2-[[2-Methyl-3-Oxidanyl-5-(Phosphonooxymethyl)pyridin-4-Yl]methylamino]-4-Sulfanyl-Butanoic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-homocysteine intermediates | PDB:7F1V | ||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | Yes | [4] |
| 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 .7XF or .7XF2 or .7XF3 or :37XF;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:93 or .A:114 or .A:117 or .A:157 or .A:161 or .A:186 or .A:188 or .A:189 or .A:208 or .A:210 or .A:211 or .A:220 or .A:221 or .A:339 or .A:340 or .A:341 or .A:355 or .A:375 or .B:50 or .B:59 or .B:61; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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SER88[A]
3.441
GLY89[A]
2.773
MET90[A]
2.834
GLY91[A]
4.991
ILE93[A]
3.677
TYR114[A]
3.046
THR117[A]
4.535
GLU157[A]
4.181
ASN161[A]
3.122
ASP186[A]
2.760
THR188[A]
3.746
TYR189[A]
4.203
SER208[A]
2.843
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| Ligand Name: (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates. | PDB:5X30 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [2] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4LM or .4LM2 or .4LM3 or :34LM;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:186 or .B:188 or .B:189 or .B:208 or .B:210 or .B:211 or .B:220 or .B:221 or .B:339 or .B:340 or .B:341 or .B:349 or .B:375; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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TYR59[A]
2.402
ARG61[A]
2.732
SER88[B]
3.388
GLY89[B]
2.756
MET90[B]
2.904
GLY91[B]
4.999
ILE93[B]
3.757
TYR114[B]
3.001
THR117[B]
4.579
GLU157[B]
4.287
ASP186[B]
2.647
THR188[B]
3.684
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal Structure of L-methionine alpha-, gamma-lyase | ||||
| REF 2 | 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 3 | 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 4 | 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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