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IPR022419 is a Porphobilinogen deaminase, dipyrromethane cofactor binding site.
<p>This entry represents the region around a cysteine residues that is conserved in porphobilinogen deaminases from various prokaryotic and eukaryotic sources. The sulphur atom of this cysteine residue has been shown in the Escherichia coli enzyme (gene hemC) to be bound to the dipyrromethane cofactor [[cite:PUB00000469]]. Porphobilinogen deaminase covalently binds a dipyrromethane cofactor to which the PBG subunits are added in a stepwise fashion. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins [[cite:PUB00029805]]. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.</p>
This description is obtained from EB-eye REST.
GO predictions are based solely on the InterPro-to-GO mappings published by EMBL-EBI, which are in turn based on the mapping of predicted domains to the InterPro dataset. The InterPro-to-GO mapping was last updated on , while the GO metadata was last updated on .
| GO term | Namespace | Name | Definition | Relationships |
|---|---|---|---|---|
| Molecular function | Hydroxymethylbilane synthase activity | Catalysis of the reaction: H(2)O + 4 porphobilinogen = hydroxymethylbilane + 4 NH(4)(+). | ||
| Biological process | Peptidyl-pyrromethane cofactor linkage | The covalent binding of a pyrromethane (dipyrrin) cofactor to protein via the sulfur atom of cysteine forming dipyrrolylmethanemethyl-L-cysteine. | ||
| Biological process | Tetrapyrrole biosynthetic process | The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. |
| Transcript | Name | Description | Predicted domains | Domain count |
|---|---|---|---|---|
| – | Porphobilinogen deaminase [Medicago truncatula] gi|357474093|ref|XP_003607331.1| | 17 | ||
| – | PREDICTED: porphobilinogen deaminase, chloroplastic-like [Glycine max] gi|356538495|ref|XP_003537739.1| | 22 | ||
| – | Porphobilinogen deaminase; TAIR: AT5G08280.1 hydroxymethylbilane synthase; Swiss-Prot: sp|Q43082|HEM3_PEA Porphobilinogen deaminase, chloroplastic; TrEMBL-Plants: tr|A0A151SCZ0|A0A151SCZ0_CAJCA Uncharacterized protein; Found in the gene: LotjaGi2g1v0443900 | 19 | ||
| – | Porphobilinogen deaminase, putative; TAIR: AT5G08280.1 hydroxymethylbilane synthase; Swiss-Prot: sp|Q43082|HEM3_PEA Porphobilinogen deaminase, chloroplastic; TrEMBL-Plants: tr|A0A151SCZ0|A0A151SCZ0_CAJCA Uncharacterized protein; Found in the gene: LotjaGi4g1v0340300 | 19 | ||
| – | Porphobilinogen deaminase, putative; TAIR: AT5G08280.1 hydroxymethylbilane synthase; Swiss-Prot: sp|Q43082|HEM3_PEA Porphobilinogen deaminase, chloroplastic; TrEMBL-Plants: tr|A0A151SCZ0|A0A151SCZ0_CAJCA Uncharacterized protein; Found in the gene: LotjaGi4g1v0340300 | 18 |
A list of co-occurring predicted domains within the L. japonicus gene space:
| Predicted domain | Source | Observations | Saturation (%) |
|---|---|---|---|
| cd13648 | CDD | 1 | 20.00 |