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1  structure 299  species 0  interactions 314  sequences 4  architectures

Family: BPL_LplA_LipB_2 (PF16917)

Summary: Biotin/lipoate A/B protein ligase family

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Biotin/lipoate A/B protein ligase family Provide feedback

No Pfam abstract.

Internal 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].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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Pfam Clan

This family is a member of clan tRNA_synt_II (CL0040), which has the following description:

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 [1] (and reference therein).

The clan contains the following 11 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 tRNA_synthFbeta

Alignments

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...

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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.

  Seed
(31)
Full
(314)
Representative proteomes UniProt
(1033)
NCBI
(7253)
Meta
(116)
RP15
(24)
RP35
(135)
RP55
(325)
RP75
(516)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(31)
Full
(314)
Representative proteomes UniProt
(1033)
NCBI
(7253)
Meta
(116)
RP15
(24)
RP35
(135)
RP55
(325)
RP75
(516)
Alignment:
Format:
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Sequence:
Gaps:
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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
(31)
Full
(314)
Representative proteomes UniProt
(1033)
NCBI
(7253)
Meta
(116)
RP15
(24)
RP35
(135)
RP55
(325)
RP75
(516)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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.

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.

Curation View help on the curation process

Seed source: PDB:3bfm
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Eberhardt R
Number in seed: 31
Number in full: 314
Average length of the domain: 175.00 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 72.06 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 183
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Selections

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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 BPL_LplA_LipB_2 domain has been found. There are 1 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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