SUPERFAMILY 1.75 HMM library and genome assignments server


Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   dsRBD-like [ 54767] (5)
Superfamily:   Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain [ 54782]
Families:   Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain [ 54783]


Superfamily statistics
Genomes (2,480) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,655 13,587 3
Proteins 2,646 13,580 3


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 4.542e-07 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 2.38e-06 Least Informative Direct
Biological Process (BP) biosynthetic process 2.343e-07 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0009949 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 3.832e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 9.222e-07 Least Informative Direct
Biological Process (BP) heterocycle biosynthetic process 1.278e-11 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 1.293e-11 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.212e-11 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 1.807e-11 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 5.867e-11 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 1.458e-12 Moderately Informative Direct
Biological Process (BP) pigment metabolic process 0 Informative Direct
Biological Process (BP) porphyrin-containing compound biosynthetic process 4.082e-05 Highly Informative Direct
Biological Process (BP) heme metabolic process 4.853e-05 Highly Informative Direct
Biological Process (BP) pigment biosynthetic process 1.836e-12 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processChlorophyll biosynthesis0Highly InformativeDirect
Biological processPorphyrin biosynthesis0Highly InformativeDirect
Biological processHeme biosynthesis5.88e-12Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)macrocycle metabolism0Moderately InformativeDirect
UniPathway (UP)porphyrin-containing compound metabolism0Moderately InformativeDirect
UniPathway (UP)pigment biosynthesis0InformativeDirect
UniPathway (UP)protoporphyrin-IX biosynthesis0InformativeDirect
UniPathway (UP)heterocycle biosynthesis1.056e-06InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR000860 SSF54782 Protein matches
Abstract

This entry represents hydroxymethylbilane synthase (or porphobilinogen deaminase, ), which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain [PubMed11215515]. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [PubMed12555854, PubMed1522882]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) [PubMed16935474].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 1 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 1 hidden Markov models representing the Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]