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109  structures 3313  species 0  interactions 4952  sequences 11  architectures

Family: UbiD (PF01977)

Summary: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase

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This is the Wikipedia entry entitled "UbiD protein domain". More...

UbiD protein domain Edit Wikipedia article

PDB 2idb EBI.jpg
crystal structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (ubid) from escherichia coli, northeast structural genomics target er459.

In molecular biology this protein domain, refers to UbiD, which is found in prokaryotes, archaea and fungi, with two members in Archaeoglobus fulgidus. They are related to UbiD, a 3-octaprenyl-4-hydroxybenzoate carboxy-lyase from Escherichia coli that is involved in ubiquinone biosynthesis.[1] The member from Helicobacter pylori has a C-terminal extension of just over 100 residues that is shared, in part, by the Aquifex aeolicus homologue.


Ubiquinone is an essential electron carrier in prokaryotes. In Escherichia coli, the Ubiquinone biosynthesis pathway involves at least nine reactions whereby 3-octaprenyl4-hydroxybenzoate decarboxylase (UbiD) is an enzyme on the pathway which catalyses the conversion of the substrate 3-octaprenyl-4-hydroxybenzoate to the product, 2-octaprenyl phenol.[2] E. coli ubiD- mutants have defects in Q8 biosynthesis, accumulate 4-hydroxy-3-octaprenylbenzoicacid (HP8B), and lack decarboxylase activity in vitro. However, E. coli ubiD- mutants retained the ability to produce about 20–25% of the normal levels of Q 4-hydroxy-3-octaprenylbenzoic acid.[3] In essence, the protein domain, UbiD, is vital to creating ubiquinone, an essential electron carrier in the creation on energy.


  1. ^ Zhang H, Javor GT (November 2000). "Identification of the ubiD gene on the Escherichia coli chromosome". J. Bacteriol. 182 (21): 6243–6. doi:10.1128/jb.182.21.6243-6246.2000. PMC 94763. PMID 11029449.
  2. ^ Liu J, Liu JH (2006). "Ubiquinone (coenzyme Q) biosynthesis in Chlamydophila pneumoniae AR39: identification of the ubiD gene". Acta Biochim Biophys Sin (Shanghai). 38 (10): 725–30. doi:10.1111/j.1745-7270.2006.00214.x. PMID 17033719.
  3. ^ Gulmezian M, Hyman KR, Marbois BN, Clarke CF, Javor GT (2007). "The role of UbiX in Escherichia coli coenzyme Q biosynthesis". Arch Biochem Biophys. 467 (2): 144–53. doi:10.1016/ PMC 2475804. PMID 17889824.
This article incorporates text from the public domain Pfam and InterPro: IPR002830

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3-octaprenyl-4-hydroxybenzoate carboxy-lyase Provide feedback

This family has been characterised as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes [1]. This enzyme catalyses the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+ [1].

Literature references

  1. Leppik RA, Young IG, Gibson F; , Biochim Biophys Acta 1976;436:800-810.: Membrane-associated reactions in ubiquinone biosynthesis in Escherichia coli. 3-Octaprenyl-4-hydroxybenzoate carboxy-lyase. PUBMED:782527 EPMC:782527

This tab holds annotation information from the InterPro database.

InterPro entry IPR002830

This family of proteins is found in prokaryotes, archaea and fungi, with two members in Archaeoglobus fulgidus. They are related to UbiD, a 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (also known as polyprenyl p-hydroxybenzoate decarboxylase) from Escherichia coli that is involved in ubiquinone biosynthesis [ PUBMED:11029449 ]. The member from Helicobacter pylori has a C-terminal extension of just over 100 residues that is shared, in part, by the Aquifex aeolicus homologue.

Proteins in this entry includes:

  • Bacterial UbiD that catalyses the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol. It is involved in ubiquinone biosynthesis [ PUBMED:11029449 ].
  • Budding yeast Fdc1 that catalyses the reversible decarboxylation of aromatic carboxylic acids like ferulic acid, p-coumaric acid or cinnamic acid, producing the corresponding vinyl derivatives 4-vinylphenol, 4-vinylguaiacol, and styrene, respectively, which play the role of aroma metabolites [ PUBMED:20471595 , PUBMED:25647642 ]. Fdc1 is not essential for ubiquinone synthesis [ PUBMED:20471595 ].
  • 4-hydroxybenzoate decarboxylase subunit C (also known as HBDC) that catalyses the reversible decarboxylation of 4-hydroxybenzoate [ PUBMED:17211544 ].
  • Phenolic acid decarboxylase subunit C (YclC) that can catalyse the reversible decarboxylation of 4-hydroxybenzoate and vanillate [ PUBMED:10438791 , PUBMED:7744052 , PUBMED:15979273 ] and can also decarboxylate 3,4-dihydroxybenzoate [ PUBMED:7744052 ].

Gene Ontology

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Domain organisation

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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Seed source: Enright A
Previous IDs: DUF117; UPF0096;
Type: Family
Sequence Ontology: SO:0100021
Author: Enright A , Ouzounis C , Bateman A
Number in seed: 397
Number in full: 4952
Average length of the domain: 389.30 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 82.11 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.8 19.8
Trusted cut-off 20.1 19.8
Noise cut-off 19.7 19.7
Model length: 406
Family (HMM) version: 18
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Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the UbiD domain has been found. There are 109 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A1D8PQ75 View 3D Structure Click here
P0AAB4 View 3D Structure Click here
Q03034 View 3D Structure Click here
Q58533 View 3D Structure Click here