Summary: Biotin/lipoate A/B protein ligase family
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This is the Wikipedia entry entitled "Cofactor transferase family". More...
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Cofactor transferase family Edit Wikipedia article
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|Cofactor transferase domain|
The three-dimensional structure of BirA, the repressor of the Escherichia coli biotin biosynthetic operon.
|Bacterial lipoate protein ligase C-terminus|
crystal structure of putative lipoate-protein ligase (np_345629.1) from streptococcus pneumoniae tigr4 at 1.99 a resolution
|Biotin protein ligase C terminal domain|
In molecular biology, the Cofactor transferase family is a family of protein domains that includes biotin protein ligases, lipoate-protein ligases A, octanoyl-(acyl carrier protein):protein N-octanoyltransferases, and lipoyl-protein:protein N-lipoyltransferases. The metabolism of the cofactors Biotin and lipoic acid share this family. They also share the target modification domain (Pfam PF00364), and the sulfur insertion enzyme (Pfam PF04055).
Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the biotin carboxyl carrier protein. Each organism likely has only one BPL protein. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine. Biotin attachment is required for biotin biosynthesis and utilization of free biotin.
Lipoate-protein ligase catalyses the formation of an amide linkage between lipoic acid and a specific lysine residue of the lipoyl domain of lipoate dependent enzymes. They are required for the utilization of free lipoic acid.
Octanoyl-(acyl carrier protein):protein N-octanoyltransferases, or octanoyltransferases, are required for lipoic acid biosynthesis. They transfer octanoate from the acyl carrier protein (ACP), part of fatty acid biosynthesis, to the specific lysine residue of lipoyl domains. Two octanoyltransferase isozymes exist in this superfamily.
Lipoyl-protein:protein N-lipoyltransferases, or lipoylamidotransferases, are required for lipoic acid metabolism in some organisms. They transfer lipoic acid or octanoate from lipoyl domains and transfer to other lipoyl domains. In Bacillus subtilis, the transfer is from the glycine cleavage system H protein, GcvH, to other lipoyl domains. This is because the octanoyltransferase of B. subtilis is specific for GcvH.
Octanoyltransferases and lipoyl-amidotransferases are single domain enzymes. Characterized lipoate protein ligases require an additional accessory domain (Pfam PF10437) to adenylate the acyl substrate. Biotin protein ligases have an additional C-terminal domain which participates in biotin adenylation and dimerization. Biotin protein ligases may also have an additional N-terminal domain required for DNA binding, although this domain is not always present.
- Wilson KP, Shewchuk LM, Brennan RG, Otsuka AJ, Matthews BW (October 1992). "Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains". Proc. Natl. Acad. Sci. U.S.A. 89 (19): 9257–61. doi:10.1073/pnas.89.19.9257. PMC . PMID 1409631.
- Reche PA (October 2000). "Lipoylating and biotinylating enzymes contain a homologous catalytic module". Protein Sci. 9 (10): 1922–9. doi:10.1110/ps.9.10.1922. PMC . PMID 11106165.
- Chapman-Smith A, Cronan JE (September 1999). "The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity". Trends Biochem. Sci. 24 (9): 359–63. doi:10.1016/s0968-0004(99)01438-3. PMID 10470036.
- Morris TW, Reed KE, Cronan JE (June 1994). "Identification of the gene encoding lipoate-protein ligase A of Escherichia coli. Molecular cloning and characterization of the lplA gene and gene product". J. Biol. Chem. 269 (23): 16091–100. PMID 8206909.
- Cronan JE, Zhao X, Jiang Y (2005). "Function, attachment and synthesis of lipoic acid in Escherichia coli". Adv. Microb. Physiol. 50: 103–46. doi:10.1016/S0065-2911(05)50003-1. PMID 16221579.
- Christensen QH, Cronan JE (2010). "Lipoic acid synthesis: a new family of octanoyltransferases generally annotated as lipoate protein ligases.". Biochemistry. 49 (46): 10024–36. doi:10.1021/bi101215f. PMC . PMID 20882995.
- Christensen QH, Martin N, Mansilla MC, de Mendoza D, Cronan JE (2011). "A novel amidotransferase required for lipoic acid cofactor assembly in Bacillus subtilis.". Mol. Microbiol. 80 (2): 350–63. doi:10.1111/j.1365-2958.2011.07598.x. PMC . PMID 21338421.
- Martin N, Christensen QH, Mansilla MC, Cronan JE, de Mendoza D (2011). "A novel two-gene requirement for the octanoyltransfer reaction of Bacillus subtilis lipoic acid biosynthesis.". Mol. Microbiol. 80 (2): 335–49. doi:10.1111/j.1365-2958.2011.07597.x. PMC . PMID 21338420.
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Biotin/lipoate A/B protein ligase family Provide feedback
This family includes biotin protein ligase, lipoate-protein ligase A and B. Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to form cellular metabolites. Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Each organism probably has only one BPL. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine . Lipoate-protein ligase A (LPLA) catalyses the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes . The unusual biosynthesis pathway of lipoic acid is mechanistically intertwined with attachment of the cofactor .
Wilson KP, Shewchuk LM, Brennan RG, Otsuka AJ, Matthews BW; , Proc Natl Acad Sci USA 1992;89:9257-9261.: Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. PUBMED:1409631 EPMC:1409631
Chapman-Smith A, Cronan JE Jr; , Trends Biochem Sci 1999;24:359-363.: The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity. PUBMED:10470036 EPMC:10470036
Morris TW, Reed KE, Cronan JE Jr; , J Biol Chem 1994;269:16091-16100.: Identification of the gene encoding lipoate-protein ligase A of Escherichia coli. Molecular cloning and characterization of the lplA gene and gene product. PUBMED:8206909 EPMC:8206909
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004143
Biotin and lipoic acid are the covalently bound cofactors of various multicomponent enzyme complexes that catalyze key metabolic reactions. In these enzymes complexes, biotin and lipoic acid are attached via amide linkage through their carboxyl group and the epsilon-amino group of a specific lysine residue of a protein module known respectively as the biotinyl and the lipoyl domain. Covalent attachment of biotin and lipoic acid to these enzyme complexes occurs post-translationally, and it is mediated by biotinylating and lipoylating protein enzymes, which specifically recognise the biotinyl and lipoyl domains, ensuring their correct post-translational modification. Lipoylating and biotinylating enzymes are evolutionarily related protein families containing a homologous catalytic module [PUBMED:11106165].
Amino acid sequence conservation between the catalytic modules of biotinyl protein ligases (BPLs) and lipoyl protein ligases (LPLs) is very low, and mainly affects residues that are important for the scaffold of the structure, such as those contributing to the hydrophobic core. Despite the poor overall sequence similarity, a single lysine residue is strictly conserved in all LPL and BPL sequences. This lysine residue is likely to bind specifically to the carbonyl oxygen of the carboxyl group of biotin or at the end of the hydrogen- carbon tail of the lipoyl moiety [PUBMED:11106165]. The BPL/LPL catalytic domain contains a seven-stranded mixed beta-sheet on one side and four alpha-helices on the other side [PUBMED:16169557].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||cellular protein modification process (GO:0006464)|
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:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
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Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
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Aminoacyl-tRNA synthetases are key components of the protein translation machinery that catalyse two basic reactions. First, the activation of amino acids via the formation of aminoacyl adenylates and second, linking the activated amino acid to the cognate tRNAs. The aminoacyl-tRNA synthetases generate AMP as the second end product of this reaction, which differentiates them from the majority of ATP-dependent enzymes that produce ADP. In addition, there is a specific aminoacyl-tRNA synthetases for each of the 20 amino acids and there are two structurally distinct classes of aminoacyl-tRNA synthetases, each encompassing 10 different specificities. The two classes have alternative modes of aminoacylation: class I aminoacylate the 2'OH of the cognate tRNA; class II aminoacylate 3'OH (with the exception of PheRS). Each class contain a conserved core domain that is involved in ATP binding and hydrolysis and combines with additional domains that determine the specificity of interactions with the cognate amino acid and tRNA. The class II core domain consist of a mixed-beta sheet, similar to that found in the biotin synthetases, hence why this family has also been included in this clan. The core domain contains three modestly conserved motifs that are responsible for ATP binding. The class II aminoacyl-tRNA synthetases can contain additional nested domains, found inserted in the loops of the core domain  (and reference therein).
The clan contains the following 10 members:AsnA BPL_LplA_LipB BPL_LplA_LipB_2 DUF366 tRNA-synt_2 tRNA-synt_2b tRNA-synt_2c tRNA-synt_2d tRNA-synt_2e tRNA-synt_His
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
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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.
Note: You can also download the data file for the tree.
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.
|Seed source:||Reche P|
|Author:||Bateman A, Reche P, Eberhardt R|
|Number in seed:||18|
|Number in full:||10146|
|Average length of the domain:||122.30 aa|
|Average identity of full alignment:||18 %|
|Average coverage of the sequence by the domain:||39.51 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|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 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.
Anomalies in the taxonomy tree
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.
Too many species/sequences
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.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
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.
You can use the tree controls to manipulate how the interactive tree is displayed:
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There are 8 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 BPL_LplA_LipB domain has been found. There are 132 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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