1GTK

Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA 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 (2022-06-29)
A	SCOP2B Superfamily	Type 2 solute binding protein-like	8033314	3000083	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Porphobil_deamC	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: Porphobil_deamC	ECOD (1.6)
A	Porphobil_deam_N	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: Porphobil_deam_N	ECOD (1.6)
A	Porphobil_deam_C	e1gtkA3	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: Porphobil_deam_C	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
A	PF03900	Porphobilinogen deaminase, C-terminal domain (Porphobil_deamC)	Porphobilinogen deaminase, C-terminal domain	-	Domain
A	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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PORPHOBILINOGEN DEAMINASE	hydroxymethylbilane synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	pigment metabolic process heme metabolic process porphyrin-containing compound biosynthetic process organonitrogen compound metabolic process tetrapyrrole metabolic process heme biosynthetic process organonitrogen compound biosynthetic process pigment biosynthetic process organic cyclic compound metabolic process organic substance metabolic process tetrapyrrole biosynthetic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process pigment metabolic process heme metabolic process porphyrin-containing compound biosynthetic process organonitrogen compound metabolic process tetrapyrrole metabolic process heme biosynthetic process organonitrogen compound biosynthetic process pigment biosynthetic process organic cyclic compound metabolic process organic substance metabolic process tetrapyrrole biosynthetic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process porphyrin-containing compound metabolic process protoporphyrinogen IX metabolic process protoporphyrinogen IX biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR022419	Porphobilinogen deaminase, dipyrromethane cofactor binding site	Binding Site
A	IPR036803	Porphobilinogen deaminase, C-terminal domain superfamily	Homologous Superfamily
A	IPR022418	Porphobilinogen deaminase, C-terminal	Domain
A	IPR000860	Porphobilinogen deaminase	Family
A	IPR022417	Porphobilinogen deaminase, N-terminal	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	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 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.5.1.61 (PDB Primary Data) Search M-CSA Motif + EC 2.5.1.61

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.