1B4K
High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004655 | molecular_function | porphobilinogen synthase activity |
| A | 0005829 | cellular_component | cytosol |
| A | 0006779 | biological_process | porphyrin-containing compound biosynthetic process |
| A | 0006782 | biological_process | protoporphyrinogen IX biosynthetic process |
| A | 0006783 | biological_process | heme biosynthetic process |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0016829 | molecular_function | lyase activity |
| A | 0033014 | biological_process | tetrapyrrole biosynthetic process |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0004655 | molecular_function | porphobilinogen synthase activity |
| B | 0005829 | cellular_component | cytosol |
| B | 0006779 | biological_process | porphyrin-containing compound biosynthetic process |
| B | 0006782 | biological_process | protoporphyrinogen IX biosynthetic process |
| B | 0006783 | biological_process | heme biosynthetic process |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0016829 | molecular_function | lyase activity |
| B | 0033014 | biological_process | tetrapyrrole biosynthetic process |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 3 |
| Details | ACTIVE SITE IN MOLECULE A |
| Chain | Residue |
| A | ASP139 |
| A | LYS205 |
| A | LYS260 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | ACTIVE SITE IN MOLECULE A |
| Chain | Residue |
| B | ASP139 |
| B | LYS205 |
| B | LYS260 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 A 401 |
| Chain | Residue |
| A | LYS205 |
| A | TYR211 |
| A | ARG215 |
| A | LYS229 |
| A | GLN233 |
| A | SHF403 |
| A | HOH582 |
| A | HOH621 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 401 |
| Chain | Residue |
| B | LYS205 |
| B | ARG215 |
| B | GLN233 |
| B | SHF402 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 402 |
| Chain | Residue |
| A | GLU245 |
| A | HOH501 |
| A | HOH502 |
| A | HOH503 |
| A | HOH504 |
| A | HOH505 |
| site_id | AC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SHF A 403 |
| Chain | Residue |
| A | LYS205 |
| A | TYR211 |
| A | PHE214 |
| A | LYS260 |
| A | TYR283 |
| A | VAL285 |
| A | SER286 |
| A | TYR324 |
| A | SO4401 |
| site_id | AC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SHF B 402 |
| Chain | Residue |
| B | TYR211 |
| B | PHE214 |
| B | LYS260 |
| B | TYR283 |
| B | VAL285 |
| B | SER286 |
| B | TYR324 |
| B | SO4401 |
| B | HOH690 |
| site_id | MG1 |
| Number of Residues | 6 |
| Details | MG2+-BINDING SITE IN MOLECULE A |
| Chain | Residue |
| A | MG402 |
| A | ASP179 |
| A | ARG181 |
| A | GLU245 |
| A | ASP249 |
| B | ARG19 |
Functional Information from PROSITE/UniProt
| site_id | PS00169 |
| Number of Residues | 13 |
| Details | D_ALA_DEHYDRATASE Delta-aminolevulinic acid dehydratase active site. GaDmVMVKPGmpY |
| Chain | Residue | Details |
| A | GLY253-TYR265 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | Active site: {"description":"Schiff-base intermediate with substrate","evidences":[{"source":"PubMed","id":"12079382","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16819823","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 9 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10356331","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12079382","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1h7o |
| Chain | Residue | Details |
| A | SER175 | |
| A | ASP127 | |
| A | LYS260 | |
| A | LYS205 |
| site_id | CSA2 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1h7o |
| Chain | Residue | Details |
| B | SER175 | |
| B | ASP127 | |
| B | LYS260 | |
| B | LYS205 |
| site_id | MCSA1 |
| Number of Residues | 2 |
| Details | M-CSA 230 |
| Chain | Residue | Details |
| A | LYS205 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, polar interaction, proton acceptor, proton donor |
| A | LYS260 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, polar interaction, proton acceptor, proton donor |
| site_id | MCSA2 |
| Number of Residues | 2 |
| Details | M-CSA 230 |
| Chain | Residue | Details |
| B | LYS205 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, polar interaction, proton acceptor, proton donor |
| B | LYS260 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, polar interaction, proton acceptor, proton donor |
