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 tetrapyrrole metabolic process heme biosynthetic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process protoporphyrinogen IX metabolic process protoporphyrinogen IX biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.