1PG8
Crystal Structure of L-methionine alpha-, gamma-lyase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0016829 | molecular_function | lyase activity |
| A | 0016846 | molecular_function | carbon-sulfur lyase activity |
| A | 0018826 | molecular_function | methionine gamma-lyase activity |
| A | 0019346 | biological_process | transsulfuration |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0047982 | molecular_function | homocysteine desulfhydrase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0016829 | molecular_function | lyase activity |
| B | 0016846 | molecular_function | carbon-sulfur lyase activity |
| B | 0018826 | molecular_function | methionine gamma-lyase activity |
| B | 0019346 | biological_process | transsulfuration |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0047982 | molecular_function | homocysteine desulfhydrase activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0016829 | molecular_function | lyase activity |
| C | 0016846 | molecular_function | carbon-sulfur lyase activity |
| C | 0018826 | molecular_function | methionine gamma-lyase activity |
| C | 0019346 | biological_process | transsulfuration |
| C | 0030170 | molecular_function | pyridoxal phosphate binding |
| C | 0047982 | molecular_function | homocysteine desulfhydrase activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0016829 | molecular_function | lyase activity |
| D | 0016846 | molecular_function | carbon-sulfur lyase activity |
| D | 0018826 | molecular_function | methionine gamma-lyase activity |
| D | 0019346 | biological_process | transsulfuration |
| D | 0030170 | molecular_function | pyridoxal phosphate binding |
| D | 0047982 | molecular_function | homocysteine desulfhydrase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1146 |
| Chain | Residue |
| C | TYR114 |
| C | LYS211 |
| C | VAL339 |
| C | SER340 |
| C | GLN349 |
| C | ARG375 |
| C | HOH1284 |
| C | HOH1285 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1124 |
| Chain | Residue |
| A | ASN161 |
| A | LYS211 |
| A | VAL339 |
| A | SER340 |
| A | ARG375 |
| A | HOH1495 |
| A | HOH1496 |
| A | TYR114 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1138 |
| Chain | Residue |
| B | TYR114 |
| B | LYS211 |
| B | VAL339 |
| B | SER340 |
| B | LEU341 |
| B | GLN349 |
| B | ARG375 |
| B | PLP1799 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1147 |
| Chain | Residue |
| D | TYR114 |
| D | LYS211 |
| D | VAL339 |
| D | SER340 |
| D | GLN349 |
| D | ARG375 |
| site_id | AC5 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PLP A 1399 |
| Chain | Residue |
| A | SER88 |
| A | GLY89 |
| A | MET90 |
| A | ILE93 |
| A | TYR114 |
| A | ASP186 |
| A | SER208 |
| A | THR210 |
| A | LYS211 |
| A | HOH1495 |
| C | TYR59 |
| C | ARG61 |
| site_id | AC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE PLP B 1799 |
| Chain | Residue |
| B | SER88 |
| B | GLY89 |
| B | MET90 |
| B | TYR114 |
| B | ASP186 |
| B | TYR189 |
| B | SER208 |
| B | THR210 |
| B | LYS211 |
| B | LEU341 |
| B | SO41138 |
| D | TYR59 |
| D | ARG61 |
| site_id | AC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PLP C 1199 |
| Chain | Residue |
| A | TYR59 |
| A | ARG61 |
| C | SER88 |
| C | GLY89 |
| C | MET90 |
| C | TYR114 |
| C | ASP186 |
| C | TYR189 |
| C | SER208 |
| C | THR210 |
| C | LYS211 |
| C | HOH1284 |
| site_id | AC8 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE PLP D 1599 |
| Chain | Residue |
| B | TYR59 |
| B | ARG61 |
| D | SER88 |
| D | GLY89 |
| D | MET90 |
| D | TYR114 |
| D | ASP186 |
| D | THR188 |
| D | TYR189 |
| D | SER208 |
| D | THR210 |
| D | LYS211 |
| D | LEU341 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PEG A 1001 |
| Chain | Residue |
| A | SER4 |
| A | LYS6 |
| A | PEG1002 |
| A | HOH1404 |
| D | ASP385 |
| site_id | BC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE PEG A 1002 |
| Chain | Residue |
| A | PRO8 |
| A | THR12 |
| A | ARG13 |
| A | HIS17 |
| A | PEG1001 |
| A | PEG1003 |
| A | HOH1404 |
| A | HOH1499 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PEG A 1003 |
| Chain | Residue |
| A | HIS16 |
| A | TYR19 |
| A | PEG1002 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PEG A 1004 |
| Chain | Residue |
| B | GLY25 |
| A | HIS24 |
| A | TYR33 |
| A | HIS57 |
| site_id | BC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PEG A 1005 |
| Chain | Residue |
| A | GLY25 |
| B | HIS24 |
| site_id | BC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE PEG B 1006 |
| Chain | Residue |
| B | GLY18 |
| B | TYR19 |
| B | HIS24 |
| B | PRO30 |
| B | PRO31 |
| B | VAL32 |
| B | PRO65 |
| B | THR66 |
| site_id | BC6 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE PEG A 1007 |
| Chain | Residue |
| A | ALA295 |
| A | SER296 |
| A | PHE297 |
| A | PRO298 |
| A | TYR300 |
| A | THR301 |
| C | ALA271 |
| C | GLN274 |
| C | VAL275 |
| C | GLU278 |
| C | HOH1281 |
| site_id | BC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PEG A 1008 |
| Chain | Residue |
| A | GLY110 |
| A | ASN111 |
| A | THR112 |
| A | LEU113 |
| A | VAL135 |
| A | ASP136 |
| A | MET137 |
| A | PHE156 |
| A | GLU157 |
| A | ALA160 |
| A | HIS165 |
| A | HOH1431 |
| site_id | BC8 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PEG C 1009 |
| Chain | Residue |
| B | ALA11 |
| B | ASN263 |
| C | ARG268 |
| C | ASN272 |
| C | LEU380 |
| C | GLU381 |
| C | ASP382 |
| C | ILE383 |
| C | HOH1265 |
| site_id | BC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PEG B 1010 |
| Chain | Residue |
| B | PRO8 |
| B | HIS17 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PEG C 1012 |
| Chain | Residue |
| B | HIS16 |
| B | ASP20 |
| C | GLN333 |
| C | LEU334 |
| C | SER336 |
| C | HOH1216 |
Functional Information from PROSITE/UniProt
| site_id | PS00868 |
| Number of Residues | 15 |
| Details | CYS_MET_METAB_PP Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. DLvvhSATKYLsGHG |
| Chain | Residue | Details |
| A | ASP203-GLY217 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|Ref.7 |
| Chain | Residue | Details |
| A | TYR59 | |
| B | TYR59 | |
| C | TYR59 | |
| D | TYR59 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | BINDING: in other chain => ECO:0000269|Ref.7 |
| Chain | Residue | Details |
| A | GLY89 | |
| A | SER208 | |
| B | GLY89 | |
| B | SER208 | |
| C | GLY89 | |
| C | SER208 | |
| D | GLY89 | |
| D | SER208 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22785484, ECO:0007744|PDB:3VK3, ECO:0007744|PDB:3VK4 |
| Chain | Residue | Details |
| A | TYR114 | |
| A | ARG375 | |
| B | TYR114 | |
| B | ARG375 | |
| C | TYR114 | |
| C | ARG375 | |
| D | TYR114 | |
| D | ARG375 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269|PubMed:17289792, ECO:0000269|PubMed:22785484, ECO:0000269|PubMed:3365412, ECO:0000269|Ref.7, ECO:0000269|Ref.8, ECO:0007744|PDB:1UKJ |
| Chain | Residue | Details |
| A | LYS211 | |
| B | LYS211 | |
| C | LYS211 | |
| D | LYS211 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| A | LYS211 | |
| A | ASP186 | |
| A | TYR114 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| B | LYS211 | |
| B | ASP186 | |
| B | TYR114 |
| site_id | CSA3 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| C | LYS211 | |
| C | ASP186 | |
| C | TYR114 |
| site_id | CSA4 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| D | LYS211 | |
| D | ASP186 | |
| D | TYR114 |
| site_id | CSA5 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| A | ARG61 | |
| C | ASP186 | |
| C | TYR114 |
| site_id | CSA6 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| D | ASP186 | |
| D | TYR114 | |
| B | ARG61 |
| site_id | CSA7 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| A | ASP186 | |
| A | TYR114 | |
| C | ARG61 |
| site_id | CSA8 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| D | ARG61 | |
| B | ASP186 | |
| B | TYR114 |
