1GTK | pdb_00001gtk

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

External Resource: Annotation


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad1gtka1 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)
Ad1gtka2 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

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyPorphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain 8035105 3001007 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyType 2 solute binding protein-like 8033314 3000083 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Ae1gtkA1 A: C-terminal subdomain in Lon-related proteases catalytic domainsX: C-terminal subdomain in Lon-related proteases catalytic domainsH: C-terminal subdomain in Lon-related proteases catalytic domainsT: DUF3197F:ECOD (20:10:01)
Ae1gtkA2 A: Four-helical up-and-down bundleX: Glycosyl hydrolase domainH: Glycosyl hydrolase domainT: LysR_substrateF:ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.40.190.10 Alpha Beta 3-Layer(aba) Sandwich D-Maltodextrin-Binding Protein domain 2CATH (4.3.0)
A3.30.160.40 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain Porphobilinogen deaminase, C-terminal domainCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF03900Porphobilinogen deaminase, C-terminal domain (Porphobil_deamC)Porphobilinogen deaminase, C-terminal domainDomain
PF01379Porphobilinogen deaminase, dipyromethane cofactor binding domain (Porphobil_deam)Porphobilinogen deaminase, dipyromethane cofactor binding domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
PORPHOBILINOGEN DEAMINASE

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR022419Porphobilinogen deaminase, dipyrromethane cofactor binding siteBinding Site
IPR036803Porphobilinogen deaminase, C-terminal domain superfamilyHomologous Superfamily
IPR022418Porphobilinogen deaminase, C-terminalDomain
IPR000860Porphobilinogen deaminaseFamily
IPR022417Porphobilinogen deaminase, N-terminalDomain

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

ChainsEnzyme NameDescriptionCatalytic 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
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Explore in 3D: M-CSA Motif Definition
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EC: 2.5.1.61 (PDB Primary Data)