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3  structures 2165  species 1  interaction 3152  sequences 3  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

UbiD
PDB 2idb EBI.jpg
crystal structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (ubid) from escherichia coli, northeast structural genomics target er459.
Identifiers
Symbol UbiD
Pfam PF01977
InterPro IPR002830

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.

Function

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.

References

  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. 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/j.abb.2007.08.009. PMC 2475804. PMID 17889824. 

This article incorporates text from the public domain Pfam and InterPro IPR002830

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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


External database links

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 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.

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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(155)
Full
(3152)
Representative proteomes NCBI
(2356)
Meta
(887)
RP15
(231)
RP35
(482)
RP55
(658)
RP75
(810)
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Format an alignment

  Seed
(155)
Full
(3152)
Representative proteomes NCBI
(2356)
Meta
(887)
RP15
(231)
RP35
(482)
RP55
(658)
RP75
(810)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(155)
Full
(3152)
Representative proteomes NCBI
(2356)
Meta
(887)
RP15
(231)
RP35
(482)
RP55
(658)
RP75
(810)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

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

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Enright A
Previous IDs: DUF117; UPF0096;
Type: Family
Author: Enright A, Ouzounis C, Bateman A
Number in seed: 155
Number in full: 3152
Average length of the domain: 380.40 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 83.80 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.8 19.8
Trusted cut-off 20.4 19.8
Noise cut-off 19.4 19.7
Model length: 407
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

UbiD

Structures

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 3 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 seqence.

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