6EXI
NAD-free crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii complexed 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 | 6 |
Details | binding site for residue NA A 501 |
Chain | Residue |
A | GLN62 |
A | MET390 |
A | HIS392 |
A | HOH672 |
A | HOH831 |
C | HOH687 |
site_id | AC2 |
Number of Residues | 20 |
Details | binding site for residue ADN A 502 |
Chain | Residue |
A | GLN62 |
A | THR63 |
A | ASP231 |
A | ASN232 |
A | HIS342 |
A | ASN385 |
A | LEU386 |
A | MET390 |
A | GLY391 |
A | HIS392 |
A | MET397 |
A | PHE401 |
A | HOH603 |
A | HOH624 |
A | HOH661 |
A | HOH711 |
A | HOH759 |
A | LEU57 |
A | HIS58 |
A | THR60 |
site_id | AC3 |
Number of Residues | 12 |
Details | binding site for residue ADN A 503 |
Chain | Residue |
A | GLY263 |
A | SER283 |
A | GLU284 |
A | VAL285 |
A | ASP286 |
A | CYS289 |
A | THR317 |
A | ASN319 |
A | ILE322 |
A | HOH722 |
A | HOH735 |
B | LYS467 |
site_id | AC4 |
Number of Residues | 6 |
Details | binding site for residue NA B 501 |
Chain | Residue |
B | GLN62 |
B | MET390 |
B | HIS392 |
B | HOH787 |
B | HOH857 |
D | HOH759 |
site_id | AC5 |
Number of Residues | 14 |
Details | binding site for residue ADN B 502 |
Chain | Residue |
B | HIS58 |
B | THR60 |
B | GLN62 |
B | THR63 |
B | LYS227 |
B | ASP231 |
B | HIS342 |
B | ASN385 |
B | LEU386 |
B | MET390 |
B | HIS392 |
B | MET397 |
B | PHE401 |
B | HOH841 |
site_id | AC6 |
Number of Residues | 12 |
Details | binding site for residue ADN B 503 |
Chain | Residue |
A | GLN454 |
A | LYS467 |
B | GLY263 |
B | GLU284 |
B | VAL285 |
B | ASP286 |
B | CYS289 |
B | THR317 |
B | ASN319 |
B | ILE322 |
B | HOH721 |
B | HOH815 |
site_id | AC7 |
Number of Residues | 6 |
Details | binding site for residue NA C 501 |
Chain | Residue |
A | HOH693 |
C | GLN62 |
C | MET390 |
C | HIS392 |
C | HOH771 |
C | HOH821 |
site_id | AC8 |
Number of Residues | 21 |
Details | binding site for residue ADN C 502 |
Chain | Residue |
C | LEU57 |
C | HIS58 |
C | THR60 |
C | GLN62 |
C | THR63 |
C | ASP231 |
C | ASN232 |
C | HIS342 |
C | LEU383 |
C | ASN385 |
C | LEU386 |
C | MET390 |
C | HIS392 |
C | MET397 |
C | PHE401 |
C | HOH601 |
C | HOH608 |
C | HOH631 |
C | HOH645 |
C | HOH749 |
C | HOH784 |
site_id | AC9 |
Number of Residues | 11 |
Details | binding site for residue ADN C 503 |
Chain | Residue |
C | VAL285 |
C | ASP286 |
C | CYS289 |
C | THR317 |
C | ASN319 |
C | ILE322 |
C | HOH728 |
C | HOH763 |
D | LYS467 |
C | GLY263 |
C | GLU284 |
site_id | AD1 |
Number of Residues | 6 |
Details | binding site for residue PEG C 504 |
Chain | Residue |
C | TRP357 |
C | ASN359 |
C | ASP365 |
C | HOH625 |
C | HOH653 |
C | HOH732 |
site_id | AD2 |
Number of Residues | 6 |
Details | binding site for residue NA D 501 |
Chain | Residue |
B | HOH732 |
D | GLN62 |
D | MET390 |
D | HIS392 |
D | HOH808 |
D | HOH821 |
site_id | AD3 |
Number of Residues | 17 |
Details | binding site for residue ADN D 502 |
Chain | Residue |
D | LEU57 |
D | HIS58 |
D | THR60 |
D | GLN62 |
D | THR63 |
D | ASP231 |
D | HIS342 |
D | ASN385 |
D | LEU386 |
D | HIS392 |
D | PHE401 |
D | HOH620 |
D | HOH640 |
D | HOH654 |
D | HOH657 |
D | HOH684 |
D | HOH692 |
site_id | AD4 |
Number of Residues | 15 |
Details | binding site for residue ADN D 503 |
Chain | Residue |
C | GLN454 |
C | LYS467 |
D | GLY263 |
D | SER283 |
D | GLU284 |
D | VAL285 |
D | ASP286 |
D | CYS289 |
D | THR317 |
D | ASN319 |
D | ILE322 |
D | HOH624 |
D | HOH699 |
D | HOH742 |
D | HOH864 |
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 |