1QJ5
Crystal structure of 7,8-diaminopelargonic acid synthase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0008483 | molecular_function | transaminase activity |
| A | 0009102 | biological_process | biotin biosynthetic process |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0008483 | molecular_function | transaminase activity |
| B | 0009102 | biological_process | biotin biosynthetic process |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K A 501 |
| Chain | Residue |
| A | VAL96 |
| A | THR99 |
| A | PRO100 |
| A | LEU103 |
| A | HOH2104 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K B 501 |
| Chain | Residue |
| B | HOH2109 |
| B | VAL96 |
| B | THR99 |
| B | PRO100 |
| B | LEU103 |
| site_id | AC3 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE PLP A 502 |
| Chain | Residue |
| A | GLY112 |
| A | SER113 |
| A | TYR144 |
| A | HIS145 |
| A | GLU211 |
| A | ASP245 |
| A | ILE247 |
| A | ALA248 |
| A | LYS274 |
| A | HOH2165 |
| A | HOH2193 |
| A | HOH2277 |
| B | THR309 |
| B | HOH2115 |
| B | HOH2116 |
| site_id | AC4 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE PLP B 502 |
| Chain | Residue |
| A | PRO308 |
| A | THR309 |
| A | HOH2110 |
| B | GLY112 |
| B | SER113 |
| B | TYR144 |
| B | HIS145 |
| B | GLU211 |
| B | ASP245 |
| B | ILE247 |
| B | ALA248 |
| B | LYS274 |
| B | HOH2119 |
| B | HOH2131 |
| B | HOH2197 |
Functional Information from PROSITE/UniProt
| site_id | PS00600 |
| Number of Residues | 38 |
| Details | AA_TRANSFER_CLASS_3 Aminotransferases class-III pyridoxal-phosphate attachment site. LIaDEIat.GFgRtGklfacehaeiap....DILclGKaltGG |
| Chain | Residue | Details |
| A | LEU242-GLY279 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12218056, ECO:0007744|PDB:1MLY, ECO:0007744|PDB:1QJ3 |
| Chain | Residue | Details |
| A | TRP52 | |
| A | LYS274 | |
| B | TRP52 | |
| B | LYS274 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12379100, ECO:0000269|PubMed:14756557, ECO:0007744|PDB:1DTY, ECO:0007744|PDB:1MGV, ECO:0007744|PDB:1QJ3, ECO:0007744|PDB:1QJ5, ECO:0007744|PDB:1S07 |
| Chain | Residue | Details |
| A | GLY112 | |
| A | PRO308 | |
| B | GLY112 | |
| B | PRO308 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:10452893 |
| Chain | Residue | Details |
| A | TYR144 | |
| B | TYR144 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12379100, ECO:0000269|PubMed:14756557, ECO:0007744|PDB:1MGV, ECO:0007744|PDB:1QJ3, ECO:0007744|PDB:1QJ5, ECO:0007744|PDB:1S07 |
| Chain | Residue | Details |
| A | ASP245 | |
| B | ASP245 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0007744|PDB:1QJ3 |
| Chain | Residue | Details |
| A | GLY307 | |
| B | GLY307 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12218056, ECO:0007744|PDB:1MLY, ECO:0007744|PDB:1MLZ, ECO:0007744|PDB:1QJ3 |
| Chain | Residue | Details |
| A | ARG391 | |
| B | ARG391 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | SITE: Participates in the substrate recognition with KAPA and in a stacking interaction with the adenine ring of SAM => ECO:0000305 |
| Chain | Residue | Details |
| A | TYR17 | |
| B | TYR17 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269|PubMed:12379100, ECO:0000269|PubMed:14756557, ECO:0007744|PDB:1DTY, ECO:0007744|PDB:1MGV, ECO:0007744|PDB:1QJ3, ECO:0007744|PDB:1QJ5, ECO:0007744|PDB:1S06, ECO:0007744|PDB:1S08, ECO:0007744|PDB:1S09, ECO:0007744|PDB:1S0A |
| Chain | Residue | Details |
| A | LYS274 | |
| B | LYS274 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| A | ASP245 | |
| A | TYR144 | |
| B | ILE83 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| A | ILE83 | |
| B | ASP245 | |
| B | TYR144 |
| site_id | CSA3 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| A | ASP245 | |
| A | LYS274 | |
| A | TYR144 |
| site_id | CSA4 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| B | ASP245 | |
| B | LYS274 | |
| B | TYR144 |
| site_id | CSA5 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| A | ASP245 | |
| A | LYS274 | |
| A | TYR168 |
| site_id | CSA6 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1b8g |
| Chain | Residue | Details |
| B | ASP245 | |
| B | LYS274 | |
| B | TYR168 |
| site_id | MCSA1 |
| Number of Residues | 4 |
| Details | M-CSA 249 |
| Chain | Residue | Details |
| A | TYR17 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| A | TYR144 | hydrogen bond acceptor, steric role, van der waals interaction |
| A | ASP245 | electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role |
| A | LYS274 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| site_id | MCSA2 |
| Number of Residues | 4 |
| Details | M-CSA 249 |
| Chain | Residue | Details |
| B | TYR17 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| B | TYR144 | hydrogen bond acceptor, steric role, van der waals interaction |
| B | ASP245 | electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role |
| B | LYS274 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
