5M67
Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenine and 2'-deoxyadenosine
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004013 | molecular_function | adenosylhomocysteinase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006730 | biological_process | one-carbon metabolic process |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0071269 | biological_process | L-homocysteine biosynthetic process |
| B | 0004013 | molecular_function | adenosylhomocysteinase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006730 | biological_process | one-carbon metabolic process |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0071269 | biological_process | L-homocysteine biosynthetic process |
| C | 0004013 | molecular_function | adenosylhomocysteinase activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0006730 | biological_process | one-carbon metabolic process |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0071269 | biological_process | L-homocysteine biosynthetic process |
| D | 0004013 | molecular_function | adenosylhomocysteinase activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0006730 | biological_process | one-carbon metabolic process |
| D | 0016787 | molecular_function | hydrolase activity |
| D | 0071269 | biological_process | L-homocysteine biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 501 |
| Chain | Residue |
| A | GLN62 |
| A | MET390 |
| A | HIS392 |
| A | HOH878 |
| A | HOH922 |
| C | HOH814 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 502 |
| Chain | Residue |
| C | HOH807 |
| D | HOH791 |
| D | HOH994 |
| A | HOH846 |
| A | HOH1038 |
| B | HOH783 |
| site_id | AC3 |
| Number of Residues | 33 |
| 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 | SER283 |
| 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 | ADE504 |
| A | HOH696 |
| A | HOH747 |
| A | HOH749 |
| A | HOH766 |
| A | HOH782 |
| A | HOH829 |
| A | HOH862 |
| B | GLN454 |
| B | LYS467 |
| B | TYR471 |
| site_id | AC4 |
| Number of Residues | 13 |
| Details | binding site for residue ADE A 504 |
| Chain | Residue |
| A | HIS58 |
| A | THR60 |
| A | GLN62 |
| A | THR63 |
| A | LEU386 |
| A | MET390 |
| A | HIS392 |
| A | MET397 |
| A | PHE401 |
| A | NAD503 |
| A | HOH604 |
| A | HOH729 |
| A | HOH835 |
| site_id | AC5 |
| Number of Residues | 10 |
| Details | binding site for residue PEG A 505 |
| Chain | Residue |
| A | ARG237 |
| A | GLN275 |
| A | HOH603 |
| A | HOH620 |
| A | HOH812 |
| A | HOH970 |
| C | ARG245 |
| C | GLN275 |
| C | ALA276 |
| C | GLY277 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue NA B 501 |
| Chain | Residue |
| B | GLN62 |
| B | MET390 |
| B | HIS392 |
| B | HOH847 |
| B | HOH899 |
| D | HOH842 |
| site_id | AC7 |
| Number of Residues | 34 |
| Details | binding site for residue NAD B 502 |
| Chain | Residue |
| B | HIS392 |
| B | ADE503 |
| B | HOH662 |
| B | HOH671 |
| B | HOH677 |
| B | HOH778 |
| B | HOH801 |
| B | HOH811 |
| B | HOH957 |
| 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 | ALA316 |
| B | THR317 |
| B | GLY318 |
| B | ASN319 |
| B | ILE322 |
| B | ILE340 |
| B | GLY341 |
| B | HIS342 |
| B | LEU383 |
| B | ASN385 |
| site_id | AC8 |
| Number of Residues | 12 |
| Details | binding site for residue ADE B 503 |
| Chain | Residue |
| B | HIS58 |
| B | THR60 |
| B | GLN62 |
| B | THR63 |
| B | MET390 |
| B | HIS392 |
| B | MET397 |
| B | PHE401 |
| B | NAD502 |
| B | HOH614 |
| B | HOH641 |
| B | HOH709 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | binding site for residue PEG B 504 |
| Chain | Residue |
| B | PHE20 |
| B | LYS23 |
| B | HOH685 |
| B | HOH766 |
| D | ILE360 |
| D | LYS361 |
| D | HOH816 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue ACT B 505 |
| Chain | Residue |
| B | ASP344 |
| B | ILE349 |
| B | ARG353 |
| B | ARG382 |
| B | HOH687 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue NA C 501 |
| Chain | Residue |
| A | HOH828 |
| C | GLN62 |
| C | MET390 |
| C | HIS392 |
| C | HOH791 |
| C | HOH878 |
| site_id | AD3 |
| Number of Residues | 33 |
| Details | binding site for residue NAD C 502 |
| Chain | Residue |
| C | THR198 |
| C | THR199 |
| C | THR200 |
| C | ASN232 |
| 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 | 3D1503 |
| C | HOH696 |
| C | HOH717 |
| C | HOH722 |
| C | HOH726 |
| C | HOH733 |
| C | HOH759 |
| C | HOH800 |
| D | GLN454 |
| D | LYS467 |
| D | TYR471 |
| site_id | AD4 |
| Number of Residues | 18 |
| Details | binding site for residue 3D1 C 503 |
| Chain | Residue |
| C | LEU57 |
| C | HIS58 |
| C | THR60 |
| C | GLN62 |
| C | THR63 |
| C | ASP135 |
| C | GLU197 |
| C | THR198 |
| C | LYS227 |
| C | ASP231 |
| C | HIS342 |
| C | LEU383 |
| C | MET390 |
| C | HIS392 |
| C | MET397 |
| C | PHE401 |
| C | NAD502 |
| C | HOH609 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue ACT C 504 |
| Chain | Residue |
| C | ASP344 |
| C | ILE349 |
| C | ARG353 |
| C | ARG382 |
| C | HOH601 |
| C | HOH645 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue NA D 501 |
| Chain | Residue |
| B | HOH815 |
| D | GLN62 |
| D | MET390 |
| D | HIS392 |
| D | HOH766 |
| D | HOH898 |
| site_id | AD7 |
| Number of Residues | 34 |
| Details | binding site for residue NAD D 502 |
| Chain | Residue |
| C | LEU450 |
| C | GLN454 |
| C | LYS467 |
| C | TYR471 |
| D | THR198 |
| D | THR199 |
| D | THR200 |
| 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 | LEU383 |
| D | ASN385 |
| D | HIS392 |
| D | 3D1503 |
| D | HOH715 |
| D | HOH724 |
| D | HOH753 |
| D | HOH782 |
| D | HOH783 |
| D | HOH803 |
| D | HOH949 |
| site_id | AD8 |
| Number of Residues | 17 |
| Details | binding site for residue 3D1 D 503 |
| Chain | Residue |
| D | HIS58 |
| D | THR60 |
| D | GLN62 |
| D | THR63 |
| D | ASP135 |
| D | GLU197 |
| D | THR198 |
| D | LYS227 |
| D | ASP231 |
| D | HIS342 |
| D | MET390 |
| D | HIS392 |
| D | MET397 |
| D | PHE401 |
| D | NAD502 |
| D | HOH609 |
| D | HOH621 |
| site_id | AD9 |
| Number of Residues | 10 |
| Details | binding site for residue PEG D 504 |
| Chain | Residue |
| B | ARG245 |
| B | GLN275 |
| B | ALA276 |
| B | GLY277 |
| D | ARG237 |
| D | GLN275 |
| D | HOH605 |
| D | HOH615 |
| D | HOH674 |
| D | HOH990 |
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 |
