1S07
Crystal Structure of the R253A Mutant 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 | 0004141 | molecular_function | dethiobiotin synthase activity |
A | 0005737 | cellular_component | cytoplasm |
A | 0008483 | molecular_function | transaminase activity |
A | 0009102 | biological_process | biotin biosynthetic process |
A | 0016740 | molecular_function | transferase activity |
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 | 0004141 | molecular_function | dethiobiotin synthase activity |
B | 0005737 | cellular_component | cytoplasm |
B | 0008483 | molecular_function | transaminase activity |
B | 0009102 | biological_process | biotin biosynthetic process |
B | 0016740 | molecular_function | transferase activity |
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 NA A 501 |
Chain | Residue |
A | VAL96 |
A | THR99 |
A | PRO100 |
A | LEU103 |
A | HOH595 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE NA B 502 |
Chain | Residue |
B | HOH685 |
B | VAL96 |
B | THR99 |
B | PRO100 |
B | LEU103 |
site_id | AC3 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE PLP A 430 |
Chain | Residue |
A | SER113 |
A | TYR144 |
A | HIS145 |
A | GLU211 |
A | ASP245 |
A | ALA248 |
A | LYS274 |
A | HOH512 |
A | HOH546 |
A | HOH566 |
A | HOH584 |
B | PRO308 |
B | THR309 |
B | IPA600 |
site_id | AC4 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PLP B 431 |
Chain | Residue |
A | PRO308 |
A | THR309 |
B | GLY112 |
B | SER113 |
B | TYR144 |
B | HIS145 |
B | GLU211 |
B | ASP245 |
B | ILE247 |
B | ALA248 |
B | LYS274 |
B | HOH643 |
B | HOH662 |
B | HOH665 |
B | HOH676 |
site_id | AC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE IPA B 600 |
Chain | Residue |
A | TYR17 |
A | PLP430 |
B | GLY307 |
B | THR309 |
B | HOH708 |
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.GFgAtGklfacehaeiap....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 | 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 |