1GTK
Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d1gtka1 | Alpha and beta proteins (a/b) | Periplasmic binding protein-like II | Periplasmic binding protein-like II | Phosphate binding protein-like | Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain | (Escherichia coli ) [TaxId: 562 ], | SCOPe (2.08) |
A | d1gtka2 | Alpha and beta proteins (a+b) | dsRBD-like | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | (Escherichia coli ) [TaxId: 562 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Porphobilinogen deaminase (hydroxymethylbilane synthase) C-terminal domain | 8035105 | 3001007 | SCOP2B (2021-05-27) |
A | SCOP2B Superfamily | Type 2 solute binding protein-like | 8033314 | 3000083 | SCOP2B (2021-05-27) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | PF03900 | e1gtkA1 | A: a+b two layers | X: dsRBD-like | H: Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain (From Topology) | T: Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | F: PF03900 | ECOD (1.6) |
A | PF01379 | e1gtkA2 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II (From Topology) | H: Periplasmic binding protein-like II (From Topology) | T: Periplasmic binding protein-like II | F: PF01379 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.40.190.10 | Alpha Beta | 3-Layer(aba) Sandwich | D-Maltodextrin-Binding Protein | domain 2 | CATH (4.3.0) |
A | 3.30.160.40 | Alpha Beta | 2-Layer Sandwich | Double Stranded RNA Binding Domain | Porphobilinogen deaminase, C-terminal domain | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF03900 | Porphobilinogen deaminase, C-terminal domain (Porphobil_deamC) | Porphobilinogen deaminase, C-terminal domain | - | Domain | |
PF01379 | Porphobilinogen deaminase, dipyromethane cofactor binding domain (Porphobil_deam) | Porphobilinogen deaminase, dipyromethane cofactor binding domain | - | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR022419 | Porphobilinogen deaminase, dipyrromethane cofactor binding site | Binding Site | |
IPR036803 | Porphobilinogen deaminase, C-terminal domain superfamily | Homologous Superfamily | |
IPR022418 | Porphobilinogen deaminase, C-terminal | Domain | |
IPR000860 | Porphobilinogen deaminase | Family | |
IPR022417 | Porphobilinogen deaminase, N-terminal | Domain |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
hydroxymethylbilane synthase M-CSA #260 | hydroxymethylbilane synthase (HemC) is involved in the tetrapolymerisation of porphobilinogen into the hydroxymethylbilane pre-uroporphyrinogen. It catalyses the reaction in a series of stepwise additions of pyrrolylmethyl groups until a hexapyrrole is present at the active centre. The terminal tetrapyrrole is then hydrolysed to yield the product, leaving a cysteine-bound dipyrrole on which assembly continues. | Defined by 7 residues: LYS:A-83ASP:A-84ARG:A-131ARG:A-132ARG:A-149ARG:A-155CYS:A-242 | EC: 2.5.1.61 (PDB Primary Data) |