4LVC
Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004013 | molecular_function | adenosylhomocysteinase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006730 | biological_process | one-carbon metabolic process |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0033353 | biological_process | S-adenosylmethionine cycle |
| B | 0004013 | molecular_function | adenosylhomocysteinase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006730 | biological_process | one-carbon metabolic process |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0033353 | biological_process | S-adenosylmethionine cycle |
| C | 0004013 | molecular_function | adenosylhomocysteinase activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0006730 | biological_process | one-carbon metabolic process |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0033353 | biological_process | S-adenosylmethionine cycle |
| D | 0004013 | molecular_function | adenosylhomocysteinase activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0006730 | biological_process | one-carbon metabolic process |
| D | 0016787 | molecular_function | hydrolase activity |
| D | 0033353 | biological_process | S-adenosylmethionine cycle |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE ADN A 501 |
| Chain | Residue |
| A | LEU57 |
| A | ASP231 |
| A | HIS342 |
| A | LEU383 |
| A | MET390 |
| A | GLY391 |
| A | HIS392 |
| A | MET397 |
| A | PHE401 |
| A | NAD503 |
| A | HIS58 |
| A | THR60 |
| A | GLN62 |
| A | THR63 |
| A | ASP135 |
| A | GLU197 |
| A | THR198 |
| A | LYS227 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NH4 A 502 |
| Chain | Residue |
| A | GLN62 |
| A | MET390 |
| A | HIS392 |
| A | HOH717 |
| A | HOH763 |
| C | HOH620 |
| site_id | AC3 |
| Number of Residues | 31 |
| Details | BINDING SITE FOR RESIDUE NAD A 503 |
| Chain | Residue |
| A | THR198 |
| A | THR199 |
| A | THR200 |
| A | ASN232 |
| A | GLY263 |
| A | ASP264 |
| A | VAL265 |
| A | GLU284 |
| A | VAL285 |
| A | ASP286 |
| A | CYS289 |
| A | THR317 |
| A | GLY318 |
| A | ASN319 |
| A | ILE322 |
| A | ILE340 |
| A | GLY341 |
| A | HIS342 |
| A | LEU383 |
| A | ASN385 |
| A | HIS392 |
| A | ADN501 |
| A | HOH604 |
| A | HOH626 |
| A | HOH641 |
| A | HOH719 |
| A | HOH787 |
| A | HOH813 |
| B | GLN454 |
| B | LYS467 |
| B | TYR471 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 504 |
| Chain | Residue |
| A | THR200 |
| A | HIS203 |
| A | GLY318 |
| A | HOH786 |
| A | HOH1009 |
| B | TYR457 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 505 |
| Chain | Residue |
| A | LEU427 |
| A | LYS429 |
| A | ASP432 |
| A | ASP469 |
| B | ARG472 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 506 |
| Chain | Residue |
| A | LYS106 |
| A | ARG246 |
| A | GLY387 |
| A | ASN388 |
| A | ALA389 |
| A | HOH1026 |
| site_id | AC7 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE ADN B 501 |
| Chain | Residue |
| B | HIS58 |
| B | THR60 |
| B | GLN62 |
| B | THR63 |
| B | ASP135 |
| B | GLU197 |
| B | THR198 |
| B | LYS227 |
| B | ASP231 |
| B | HIS342 |
| B | MET390 |
| B | GLY391 |
| B | HIS392 |
| B | MET397 |
| B | PHE401 |
| B | NAD503 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NH4 B 502 |
| Chain | Residue |
| B | GLN62 |
| B | MET390 |
| B | HIS392 |
| B | HOH635 |
| B | HOH756 |
| D | HOH630 |
| site_id | AC9 |
| Number of Residues | 32 |
| Details | BINDING SITE FOR RESIDUE NAD B 503 |
| Chain | Residue |
| B | THR200 |
| B | ASN232 |
| B | GLY261 |
| B | GLY263 |
| B | ASP264 |
| B | VAL265 |
| B | SER283 |
| B | GLU284 |
| B | VAL285 |
| B | ASP286 |
| B | CYS289 |
| B | THR317 |
| B | GLY318 |
| B | ASN319 |
| B | ILE322 |
| B | ILE340 |
| B | GLY341 |
| B | HIS342 |
| B | ASN385 |
| B | HIS392 |
| B | ADN501 |
| B | HOH628 |
| B | HOH631 |
| B | HOH644 |
| B | HOH713 |
| B | HOH735 |
| B | HOH741 |
| A | GLN454 |
| A | LYS467 |
| A | TYR471 |
| B | THR198 |
| B | THR199 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 504 |
| Chain | Residue |
| A | ARG472 |
| B | VAL426 |
| B | LEU427 |
| B | LYS429 |
| B | ASP432 |
| B | ASP469 |
| site_id | BC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL B 505 |
| Chain | Residue |
| A | LYS452 |
| A | ASP453 |
| B | PRO33 |
| B | GLU40 |
| B | HOH679 |
| B | HOH697 |
| B | HOH761 |
| site_id | BC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 506 |
| Chain | Residue |
| B | LYS106 |
| B | ARG246 |
| B | GLY387 |
| B | ASN388 |
| B | ALA389 |
| B | HOH645 |
| B | HOH690 |
| B | HOH819 |
| site_id | BC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 507 |
| Chain | Residue |
| B | GLY254 |
| B | ARG279 |
| C | ALA294 |
| C | TYR298 |
| C | GLU299 |
| C | VAL300 |
| D | ILE443 |
| D | GLY444 |
| site_id | BC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE ACT B 508 |
| Chain | Residue |
| B | LYS106 |
| B | GLN363 |
| site_id | BC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE ACT B 509 |
| Chain | Residue |
| B | GLY459 |
| site_id | BC7 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE ADN C 501 |
| Chain | Residue |
| C | HIS58 |
| C | THR60 |
| C | GLN62 |
| C | THR63 |
| C | ASP135 |
| C | GLU197 |
| C | THR198 |
| C | LYS227 |
| C | ASP231 |
| C | HIS342 |
| C | MET390 |
| C | HIS392 |
| C | MET397 |
| C | PHE401 |
| C | NAD503 |
| site_id | BC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NH4 C 502 |
| Chain | Residue |
| A | HOH663 |
| C | GLN62 |
| C | MET390 |
| C | HIS392 |
| C | HOH676 |
| C | HOH722 |
| site_id | BC9 |
| Number of Residues | 32 |
| Details | BINDING SITE FOR RESIDUE NAD C 503 |
| Chain | Residue |
| C | THR198 |
| C | THR199 |
| C | THR200 |
| C | ASN232 |
| C | GLY261 |
| C | GLY263 |
| C | ASP264 |
| C | VAL265 |
| C | SER283 |
| C | GLU284 |
| C | VAL285 |
| C | ASP286 |
| C | CYS289 |
| C | THR317 |
| C | GLY318 |
| C | ASN319 |
| C | ILE322 |
| C | ILE340 |
| C | GLY341 |
| C | HIS342 |
| C | LEU383 |
| C | ASN385 |
| C | HIS392 |
| C | ADN501 |
| C | HOH606 |
| C | HOH613 |
| C | HOH622 |
| C | HOH743 |
| C | HOH750 |
| C | HOH766 |
| D | LYS467 |
| D | TYR471 |
| site_id | CC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL C 504 |
| Chain | Residue |
| C | LEU427 |
| C | LYS429 |
| C | ASP432 |
| C | ASP469 |
| D | ARG472 |
| site_id | CC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL C 505 |
| Chain | Residue |
| A | HOH1026 |
| C | LYS106 |
| C | ARG246 |
| C | GLY387 |
| C | ASN388 |
| C | ALA389 |
| C | HOH739 |
| C | HOH845 |
| site_id | CC3 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL C 506 |
| Chain | Residue |
| B | ARG274 |
| B | GLY297 |
| C | ARG274 |
| C | GLY277 |
| C | CYS278 |
| C | ARG279 |
| C | HOH619 |
| C | HOH725 |
| C | HOH765 |
| C | HOH820 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL C 507 |
| Chain | Residue |
| C | GLY459 |
| C | PRO465 |
| C | LYS467 |
| C | HOH679 |
| C | HOH883 |
| site_id | CC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE ACT C 508 |
| Chain | Residue |
| C | ASP344 |
| C | ARG353 |
| C | HOH690 |
| site_id | CC6 |
| Number of Residues | 29 |
| Details | BINDING SITE FOR RESIDUE NAD D 501 |
| Chain | Residue |
| C | LYS467 |
| C | TYR471 |
| D | ASP231 |
| D | ASN232 |
| D | GLY263 |
| D | ASP264 |
| D | VAL265 |
| D | SER283 |
| D | GLU284 |
| D | VAL285 |
| D | ASP286 |
| D | CYS289 |
| D | THR317 |
| D | GLY318 |
| D | ASN319 |
| D | ILE322 |
| D | ILE340 |
| D | GLY341 |
| D | HIS342 |
| D | ASN385 |
| D | HIS392 |
| D | HOH713 |
| D | HOH717 |
| D | HOH718 |
| D | HOH720 |
| D | HOH728 |
| D | HOH780 |
| D | HOH813 |
| D | HOH825 |
| site_id | CC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL D 502 |
| Chain | Residue |
| C | HOH926 |
| D | LEU427 |
| D | LYS429 |
| D | ASP432 |
| D | ASP469 |
| D | HOH743 |
| D | HOH811 |
| site_id | CC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL D 503 |
| Chain | Residue |
| D | ASN83 |
| D | ILE84 |
| D | TYR113 |
| D | ASP138 |
| D | GLU164 |
| site_id | CC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL D 504 |
| Chain | Residue |
| D | LEU233 |
| D | ARG237 |
| D | ALA271 |
| D | HOH732 |
| D | HOH735 |
| D | HOH818 |
| D | HOH847 |
| site_id | DC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL D 505 |
| Chain | Residue |
| C | GLU449 |
| C | LEU450 |
| C | GLN462 |
| C | HOH658 |
| D | LYS452 |
| D | ASP456 |
| D | HOH973 |
Functional Information from PROSITE/UniProt
| site_id | PS00738 |
| Number of Residues | 15 |
| Details | ADOHCYASE_1 S-adenosyl-L-homocysteine hydrolase signature 1. SCNiYSTQDhAAAAI |
| Chain | Residue | Details |
| A | SER81-ILE95 |
| site_id | PS00739 |
| Number of Residues | 18 |
| Details | ADOHCYASE_2 S-adenosyl-L-homocysteine hydrolase signature 2. GKvamVaGFGdVGKGsaA |
| Chain | Residue | Details |
| A | GLY254-ALA271 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:26627650 |
| Chain | Residue | Details |
| A | HIS58 | |
| D | HIS58 | |
| D | HIS342 | |
| D | HIS392 | |
| A | HIS342 | |
| A | HIS392 | |
| B | HIS58 | |
| B | HIS342 | |
| B | HIS392 | |
| C | HIS58 | |
| C | HIS342 | |
| C | HIS392 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00563, ECO:0000305|PubMed:26627650 |
| Chain | Residue | Details |
| A | ASP135 | |
| C | GLU197 | |
| C | LYS227 | |
| C | ASP231 | |
| D | ASP135 | |
| D | GLU197 | |
| D | LYS227 | |
| D | ASP231 | |
| A | GLU197 | |
| A | LYS227 | |
| A | ASP231 | |
| B | ASP135 | |
| B | GLU197 | |
| B | LYS227 | |
| B | ASP231 | |
| C | ASP135 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 20 |
| Details | BINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_00563, ECO:0000269|PubMed:26627650 |
| Chain | Residue | Details |
| A | THR198 | |
| B | ASN385 | |
| C | THR198 | |
| C | ASN232 | |
| C | GLU284 | |
| C | ILE340 | |
| C | ASN385 | |
| D | THR198 | |
| D | ASN232 | |
| D | GLU284 | |
| D | ILE340 | |
| A | ASN232 | |
| D | ASN385 | |
| A | GLU284 | |
| A | ILE340 | |
| A | ASN385 | |
| B | THR198 | |
| B | ASN232 | |
| B | GLU284 | |
| B | ILE340 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | BINDING: in other chain => ECO:0000269|PubMed:26627650 |
| Chain | Residue | Details |
| A | VAL265 | |
| B | VAL265 | |
| C | VAL265 | |
| D | VAL265 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | BINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_00563 |
| Chain | Residue | Details |
| A | ASN319 | |
| B | ASN319 | |
| C | ASN319 | |
| D | ASN319 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:26627650 |
| Chain | Residue | Details |
| A | LYS467 | |
| A | TYR471 | |
| B | LYS467 | |
| B | TYR471 | |
| C | LYS467 | |
| C | TYR471 | |
| D | LYS467 | |
| D | TYR471 |
