Summary: Bacitracin resistance protein BacA
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This is the Wikipedia entry entitled "Undecaprenyl-diphosphatase". More...
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Undecaprenyl-diphosphatase Edit Wikipedia article
In enzymology, an undecaprenyl-diphosphatase (EC 126.96.36.199) is an enzyme that catalyzes the chemical reaction
- undecaprenyl diphosphate + H2O undecaprenyl phosphate + phosphate
Thus, the two substrates of this enzyme are undecaprenyl diphosphate and H2O, whereas its two products are undecaprenyl phosphate and phosphate.
This enzyme belongs to the family of hydrolases, specifically those acting on acid anhydrides in phosphorus-containing anhydrides. The systematic name of this enzyme class is undecaprenyl-diphosphate phosphohydrolase. Other names in common use include C55-isoprenyl diphosphatase, C55-isoprenyl pyrophosphatase, and isoprenyl pyrophosphatase. This enzyme participates in peptidoglycan biosynthesis.
- Goldman R, Strominger JL (1972). "Purification and properties of C 55 -isoprenylpyrophosphate phosphatase from Micrococcus lysodeikticus". J. Biol. Chem. 247: 5116â€“22. PMIDÂ 4341539.
- The CAS registry number for this enzyme class is Template:CAS registry.
Gene Ontology (GO) codes
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Bacitracin resistance protein BacA Provide feedback
Bacitracin resistance protein (BacA) is a putative undecaprenol kinase. BacA confers resistance to bacitracin, probably by phosphorylation of undecaprenol . More recent studies show that BacA has undecaprenyl pyrophosphate phosphatase activity. Undecaprenyl phosphate is a key lipid intermediate involved in the synthesis of various bacterial cell wall polymers. Bacitracin, a mixture of related cyclic polypeptide antibiotics, is used to treat surface tissue infections. Its primary mode of action is the inhibition of bacterial cell wall synthesis through sequestration of the essential carrier lipid undecaprenyl pyrophosphate, C55-PP, resulting in the loss of cell integrity and lysis [2,3]. The characteristic phosphatase sequence-motif in this family is likely to be the PGxSRSGG, compared with the PSGH of the PAP family of phosphatases .
Cain BD, Norton PJ, Eubanks W, Nick HS, Allen CM; , J Bacteriol 1993;175:3784-3789.: Amplification of the bacA gene confers bacitracin resistance to Escherichia coli. PUBMED:8389741 EPMC:8389741
El Ghachi M, Bouhss A, Blanot D, Mengin-Lecreulx D;, J Biol Chem. 2004;279:30106-30113.: The bacA gene of Escherichia coli encodes an undecaprenyl pyrophosphate phosphatase activity. PUBMED:15138271 EPMC:15138271
El Ghachi M, Derbise A, Bouhss A, Mengin-Lecreulx D;, J Biol Chem. 2005;280:18689-18695.: Identification of multiple genes encoding membrane proteins with undecaprenyl pyrophosphate phosphatase (UppP) activity in Escherichia coli. PUBMED:15778224 EPMC:15778224
Internal database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003824
This is a family of small, highly hydrophobic proteins. Over-expression of this protein in Escherichia coli is associated with bacitracin resistance [ PUBMED:8389741 ], and the protein was originally proposed to be an undecaprenol kinase called bacA. BacA protein, however, does not show undecaprenol phosphokinase activity [ PUBMED:15138271 ]. It is now known to be an undecaprenyl pyrophosphate phosphatase ( EC ) and is renamed UppP. It is not the only protein associated with bacitracin resistance [ PUBMED:15946938 , PUBMED:15778224 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
|Molecular function||undecaprenyl-diphosphatase activity (GO:0050380)|
|Biological process||dephosphorylation (GO:0016311)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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This family is a member of clan LysE (CL0292), which has the following description:
This clan includes a diverse range of transporter families .
The clan contains the following 19 members:BacA Cad Colicin_V DsbD DsbD_2 DUF475 DUF6044 FTR1 HupE_UreJ HupE_UreJ_2 LysE MarC Mntp NicO OFeT_1 SfLAP TauE TerC UPF0016
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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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|Author:||Mian N , Bateman A|
|Number in seed:||815|
|Number in full:||8870|
|Average length of the domain:||255 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||93.23 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||21|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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 BacA domain has been found. There are 5 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.