5M66
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 |
| A | 0071269 | biological_process | L-homocysteine biosynthetic process |
| 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 |
| B | 0071269 | biological_process | L-homocysteine biosynthetic process |
| 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 |
| C | 0071269 | biological_process | L-homocysteine biosynthetic process |
| 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 |
| D | 0071269 | biological_process | L-homocysteine biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 31 |
| Details | binding site for residue NAD A 501 |
| Chain | Residue |
| A | THR198 |
| A | SER283 |
| A | GLU284 |
| A | VAL285 |
| A | ASP286 |
| A | CYS289 |
| A | THR317 |
| A | GLY318 |
| A | ASN319 |
| A | ILE322 |
| A | ILE340 |
| A | THR199 |
| A | GLY341 |
| A | HIS342 |
| A | ASN385 |
| A | HIS392 |
| A | ADN502 |
| A | HOH637 |
| A | HOH679 |
| A | HOH683 |
| A | HOH778 |
| B | LYS467 |
| A | THR200 |
| B | TYR471 |
| B | PEG505 |
| A | ASP231 |
| A | ASN232 |
| A | GLY261 |
| A | GLY263 |
| A | ASP264 |
| A | VAL265 |
| site_id | AC2 |
| Number of Residues | 15 |
| Details | binding site for residue ADN A 502 |
| Chain | Residue |
| A | LEU57 |
| A | HIS58 |
| A | THR60 |
| A | GLN62 |
| A | THR63 |
| A | ASP135 |
| A | GLU197 |
| A | THR198 |
| A | LYS227 |
| A | ASP231 |
| A | MET390 |
| A | HIS392 |
| A | MET397 |
| A | PHE401 |
| A | NAD501 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 503 |
| Chain | Residue |
| A | GLN62 |
| A | MET390 |
| A | HIS392 |
| A | HOH670 |
| A | HOH729 |
| A | HOH767 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue PEG A 504 |
| Chain | Residue |
| A | GLU410 |
| A | TYR420 |
| A | PRO428 |
| site_id | AC5 |
| Number of Residues | 32 |
| Details | binding site for residue NAD B 501 |
| Chain | Residue |
| A | GLN454 |
| A | LYS467 |
| A | TYR471 |
| B | THR198 |
| B | THR199 |
| 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 | LEU383 |
| B | ASN385 |
| B | HIS392 |
| B | ADN502 |
| B | HOH686 |
| B | HOH694 |
| B | HOH721 |
| B | HOH730 |
| B | HOH734 |
| site_id | AC6 |
| Number of Residues | 15 |
| Details | binding site for residue ADN B 502 |
| Chain | Residue |
| B | MET397 |
| B | PHE401 |
| B | NAD501 |
| B | LEU57 |
| B | HIS58 |
| B | THR60 |
| B | GLN62 |
| B | THR63 |
| B | ASP135 |
| B | GLU197 |
| B | THR198 |
| B | LYS227 |
| B | ASP231 |
| B | MET390 |
| B | HIS392 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue NA B 503 |
| Chain | Residue |
| B | GLN62 |
| B | MET390 |
| B | HIS392 |
| B | HOH757 |
| B | HOH773 |
| D | HOH638 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue PEG B 504 |
| Chain | Residue |
| A | HIS203 |
| B | VAL460 |
| B | SER468 |
| B | HOH660 |
| site_id | AC9 |
| Number of Residues | 9 |
| Details | binding site for residue PEG B 505 |
| Chain | Residue |
| A | HIS203 |
| A | ASP223 |
| A | NAD501 |
| A | HOH626 |
| A | HOH684 |
| B | SER468 |
| B | HIS470 |
| B | TYR471 |
| B | HOH739 |
| site_id | AD1 |
| Number of Residues | 32 |
| Details | binding site for residue NAD C 501 |
| Chain | Residue |
| C | THR198 |
| C | THR199 |
| C | THR200 |
| C | ASP231 |
| 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 | ADN502 |
| C | HOH643 |
| C | HOH683 |
| C | HOH704 |
| C | HOH723 |
| C | HOH733 |
| D | LYS467 |
| D | TYR471 |
| site_id | AD2 |
| Number of Residues | 16 |
| Details | binding site for residue ADN C 502 |
| Chain | Residue |
| C | HIS58 |
| C | THR60 |
| C | GLN62 |
| C | THR63 |
| C | ASP135 |
| C | GLU197 |
| C | THR198 |
| C | LYS227 |
| C | ASP231 |
| C | LEU386 |
| C | MET390 |
| C | HIS392 |
| C | MET397 |
| C | PHE401 |
| C | NAD501 |
| C | HOH647 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue NA C 503 |
| Chain | Residue |
| A | HOH704 |
| C | GLN62 |
| C | MET390 |
| C | HIS392 |
| C | HOH709 |
| C | HOH746 |
| site_id | AD4 |
| Number of Residues | 3 |
| Details | binding site for residue PEG C 504 |
| Chain | Residue |
| C | LYS467 |
| C | SER468 |
| C | HOH633 |
| site_id | AD5 |
| Number of Residues | 3 |
| Details | binding site for residue PEG C 505 |
| Chain | Residue |
| C | MET141 |
| C | GLU165 |
| C | ARG204 |
| site_id | AD6 |
| Number of Residues | 30 |
| Details | binding site for residue NAD D 501 |
| Chain | Residue |
| C | LYS467 |
| C | TYR471 |
| D | THR198 |
| D | THR199 |
| D | THR200 |
| 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 | ADN502 |
| D | HOH615 |
| D | HOH622 |
| D | HOH657 |
| D | HOH695 |
| D | HOH721 |
| site_id | AD7 |
| Number of Residues | 17 |
| Details | binding site for residue ADN D 502 |
| Chain | Residue |
| D | HIS58 |
| D | THR60 |
| D | GLN62 |
| D | THR63 |
| D | ASP135 |
| D | GLU197 |
| D | THR198 |
| D | LYS227 |
| D | ASP231 |
| D | LEU383 |
| D | MET390 |
| D | HIS392 |
| D | MET397 |
| D | PHE401 |
| D | NAD501 |
| D | NA503 |
| D | HOH635 |
| site_id | AD8 |
| Number of Residues | 7 |
| Details | binding site for residue NA D 503 |
| Chain | Residue |
| B | HOH663 |
| D | GLN62 |
| D | MET390 |
| D | HIS392 |
| D | ADN502 |
| D | HOH714 |
| D | HOH732 |
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 | 24 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"26627650","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 16 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00563","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"26627650","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 28 |
| Details | Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_00563","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"26627650","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"26627650","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_00563","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"26627650","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
