3DHY
Crystal Structures of Mycobacterium tuberculosis S-Adenosyl-L-Homocysteine Hydrolase in Ternary Complex with Substrate and Inhibitors
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0004013 | molecular_function | adenosylhomocysteinase activity |
A | 0005515 | molecular_function | protein binding |
A | 0005576 | cellular_component | extracellular region |
A | 0005737 | cellular_component | cytoplasm |
A | 0005829 | cellular_component | cytosol |
A | 0005886 | cellular_component | plasma membrane |
A | 0006730 | biological_process | one-carbon metabolic process |
A | 0009087 | biological_process | methionine catabolic process |
A | 0009274 | cellular_component | peptidoglycan-based cell wall |
A | 0016787 | molecular_function | hydrolase activity |
A | 0033353 | biological_process | S-adenosylmethionine cycle |
A | 0035375 | molecular_function | zymogen binding |
A | 0035635 | biological_process | entry of bacterium into host cell |
A | 0044650 | biological_process | adhesion of symbiont to host cell |
A | 0046085 | biological_process | adenosine metabolic process |
A | 0070403 | molecular_function | NAD+ binding |
A | 0071269 | biological_process | L-homocysteine biosynthetic process |
B | 0004013 | molecular_function | adenosylhomocysteinase activity |
B | 0005515 | molecular_function | protein binding |
B | 0005576 | cellular_component | extracellular region |
B | 0005737 | cellular_component | cytoplasm |
B | 0005829 | cellular_component | cytosol |
B | 0005886 | cellular_component | plasma membrane |
B | 0006730 | biological_process | one-carbon metabolic process |
B | 0009087 | biological_process | methionine catabolic process |
B | 0009274 | cellular_component | peptidoglycan-based cell wall |
B | 0016787 | molecular_function | hydrolase activity |
B | 0033353 | biological_process | S-adenosylmethionine cycle |
B | 0035375 | molecular_function | zymogen binding |
B | 0035635 | biological_process | entry of bacterium into host cell |
B | 0044650 | biological_process | adhesion of symbiont to host cell |
B | 0046085 | biological_process | adenosine metabolic process |
B | 0070403 | molecular_function | NAD+ binding |
B | 0071269 | biological_process | L-homocysteine biosynthetic process |
C | 0004013 | molecular_function | adenosylhomocysteinase activity |
C | 0005515 | molecular_function | protein binding |
C | 0005576 | cellular_component | extracellular region |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0005886 | cellular_component | plasma membrane |
C | 0006730 | biological_process | one-carbon metabolic process |
C | 0009087 | biological_process | methionine catabolic process |
C | 0009274 | cellular_component | peptidoglycan-based cell wall |
C | 0016787 | molecular_function | hydrolase activity |
C | 0033353 | biological_process | S-adenosylmethionine cycle |
C | 0035375 | molecular_function | zymogen binding |
C | 0035635 | biological_process | entry of bacterium into host cell |
C | 0044650 | biological_process | adhesion of symbiont to host cell |
C | 0046085 | biological_process | adenosine metabolic process |
C | 0070403 | molecular_function | NAD+ binding |
C | 0071269 | biological_process | L-homocysteine biosynthetic process |
D | 0004013 | molecular_function | adenosylhomocysteinase activity |
D | 0005515 | molecular_function | protein binding |
D | 0005576 | cellular_component | extracellular region |
D | 0005737 | cellular_component | cytoplasm |
D | 0005829 | cellular_component | cytosol |
D | 0005886 | cellular_component | plasma membrane |
D | 0006730 | biological_process | one-carbon metabolic process |
D | 0009087 | biological_process | methionine catabolic process |
D | 0009274 | cellular_component | peptidoglycan-based cell wall |
D | 0016787 | molecular_function | hydrolase activity |
D | 0033353 | biological_process | S-adenosylmethionine cycle |
D | 0035375 | molecular_function | zymogen binding |
D | 0035635 | biological_process | entry of bacterium into host cell |
D | 0044650 | biological_process | adhesion of symbiont to host cell |
D | 0046085 | biological_process | adenosine metabolic process |
D | 0070403 | molecular_function | NAD+ binding |
D | 0071269 | biological_process | L-homocysteine biosynthetic process |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE 3DH A 500 |
Chain | Residue |
A | HIS69 |
A | LEU407 |
A | THR414 |
A | GLY415 |
A | HIS416 |
A | MET421 |
A | PHE425 |
A | THR71 |
A | GLN73 |
A | THR74 |
A | ASP156 |
A | GLU218 |
A | THR219 |
A | LYS248 |
A | ASP252 |
site_id | AC2 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE NAD A 550 |
Chain | Residue |
A | THR219 |
A | THR220 |
A | THR221 |
A | ASN253 |
A | GLY282 |
A | GLY284 |
A | ASP285 |
A | THR304 |
A | GLU305 |
A | ILE306 |
A | ASN310 |
A | THR338 |
A | GLY339 |
A | ASN340 |
A | ILE343 |
A | ILE361 |
A | GLY362 |
A | HIS363 |
A | LEU407 |
A | ASN409 |
A | HIS416 |
B | GLN476 |
B | LYS489 |
B | TYR493 |
site_id | AC3 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE 3DH B 500 |
Chain | Residue |
B | LEU68 |
B | HIS69 |
B | THR71 |
B | GLN73 |
B | THR74 |
B | ASP156 |
B | GLU218 |
B | THR219 |
B | LYS248 |
B | ASP252 |
B | GLY362 |
B | THR414 |
B | HIS416 |
B | MET421 |
site_id | AC4 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE NAD B 550 |
Chain | Residue |
A | GLN476 |
A | LYS489 |
A | TYR493 |
B | THR219 |
B | THR220 |
B | THR221 |
B | ASN253 |
B | GLY282 |
B | GLY284 |
B | ASP285 |
B | THR304 |
B | GLU305 |
B | ILE306 |
B | ASP307 |
B | ASN310 |
B | THR338 |
B | GLY339 |
B | ASN340 |
B | ILE343 |
B | ILE361 |
B | GLY362 |
B | HIS363 |
B | LEU407 |
B | ASN409 |
B | HIS416 |
site_id | AC5 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE 3DH C 500 |
Chain | Residue |
C | HIS69 |
C | THR71 |
C | GLN73 |
C | THR74 |
C | ASP156 |
C | GLU218 |
C | THR219 |
C | LYS248 |
C | ASP252 |
C | LEU407 |
C | LEU410 |
C | THR414 |
C | HIS416 |
C | MET421 |
C | PHE425 |
site_id | AC6 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE NAD C 550 |
Chain | Residue |
C | THR304 |
C | GLU305 |
C | ILE306 |
C | ASP307 |
C | THR338 |
C | GLY339 |
C | ASN340 |
C | ILE343 |
C | ILE361 |
C | GLY362 |
C | HIS363 |
C | ASN409 |
C | HIS416 |
D | GLN476 |
D | LYS489 |
D | TYR493 |
C | THR219 |
C | THR220 |
C | THR221 |
C | ASN253 |
C | GLY284 |
C | ASP285 |
site_id | AC7 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE 3DH D 500 |
Chain | Residue |
D | LEU68 |
D | HIS69 |
D | THR71 |
D | GLN73 |
D | THR74 |
D | ASP156 |
D | GLU218 |
D | THR219 |
D | LYS248 |
D | ASP252 |
D | LEU407 |
D | LEU410 |
D | THR414 |
D | GLY415 |
D | HIS416 |
D | MET421 |
D | PHE425 |
site_id | AC8 |
Number of Residues | 23 |
Details | BINDING SITE FOR RESIDUE NAD D 550 |
Chain | Residue |
C | GLN476 |
C | LYS489 |
C | TYR493 |
D | THR219 |
D | THR220 |
D | THR221 |
D | ASN253 |
D | GLY282 |
D | GLY284 |
D | ASP285 |
D | THR304 |
D | GLU305 |
D | ILE306 |
D | ASP307 |
D | THR338 |
D | GLY339 |
D | ASN340 |
D | ILE343 |
D | ILE361 |
D | GLY362 |
D | HIS363 |
D | ASN409 |
D | HIS416 |
Functional Information from PROSITE/UniProt
site_id | PS00738 |
Number of Residues | 15 |
Details | ADOHCYASE_1 S-adenosyl-L-homocysteine hydrolase signature 1. SCNiFSTQDhAAAAV |
Chain | Residue | Details |
A | SER92-VAL106 |
site_id | PS00739 |
Number of Residues | 17 |
Details | ADOHCYASE_2 S-adenosyl-L-homocysteine hydrolase signature 2. GKkvlIcGYGdVGKGc.A |
Chain | Residue | Details |
A | GLY275-ALA291 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 48 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00563 |
Chain | Residue | Details |
A | THR71 | |
A | ASN340 | |
A | ILE361 | |
A | ASN409 | |
B | THR71 | |
B | ASP156 | |
B | GLU218 | |
B | THR219 | |
B | LYS248 | |
B | ASP252 | |
B | ASN253 | |
A | ASP156 | |
B | GLY282 | |
B | GLU305 | |
B | ASN340 | |
B | ILE361 | |
B | ASN409 | |
C | THR71 | |
C | ASP156 | |
C | GLU218 | |
C | THR219 | |
C | LYS248 | |
A | GLU218 | |
C | ASP252 | |
C | ASN253 | |
C | GLY282 | |
C | GLU305 | |
C | ASN340 | |
C | ILE361 | |
C | ASN409 | |
D | THR71 | |
D | ASP156 | |
D | GLU218 | |
A | THR219 | |
D | THR219 | |
D | LYS248 | |
D | ASP252 | |
D | ASN253 | |
D | GLY282 | |
D | GLU305 | |
D | ASN340 | |
D | ILE361 | |
D | ASN409 | |
A | LYS248 | |
A | ASP252 | |
A | ASN253 | |
A | GLY282 | |
A | GLU305 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
Details | CROSSLNK: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup) => ECO:0000269|PubMed:20066036 |
Chain | Residue | Details |
A | LYS474 | |
B | LYS474 | |
C | LYS474 | |
D | LYS474 |