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113  structures 4791  species 4  interactions 11826  sequences 48  architectures

Family: BPL_LplA_LipB (PF03099)

Summary: Biotin/lipoate A/B protein ligase family

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This is the Wikipedia entry entitled "Cofactor transferase family". More...

Cofactor transferase family Edit Wikipedia article

Cofactor transferase domain
PDB 1bia EBI.jpg
The three-dimensional structure of BirA, the repressor of the Escherichia coli biotin biosynthetic operon.[1]
Identifiers
Symbol BPL
Pfam PF03099
InterPro IPR004143
SCOP 1bia
SUPERFAMILY 1bia
Bacterial lipoate protein ligase C-terminus
PDB 1vqz EBI.jpg
crystal structure of putative lipoate-protein ligase (np_345629.1) from streptococcus pneumoniae tigr4 at 1.99 a resolution
Identifiers
Symbol Lip_prot_lig_C
Pfam PF10437
InterPro IPR019491
Biotin protein ligase C terminal domain
Identifiers
Symbol BPL_C
Pfam PF02237
Pfam clan CL0206
InterPro IPR003142
SCOP 1bia
SUPERFAMILY 1bia

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.[2] 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.[3]

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.[4]

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.[5] Two octanoyltransferase isozymes exist in this superfamily.[6]

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.[7][8]

Structure[edit]

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.[1][2]

References[edit]

  1. ^ a b 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 50105. PMID 1409631. 
  2. ^ a b 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 2144473. PMID 11106165. 
  3. ^ 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. PMID 10470036. 
  4. ^ 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. 
  5. ^ 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. 
  6. ^ 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 2982868. PMID 20882995. 
  7. ^ 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 3088481. PMID 21338421. 
  8. ^ 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 3086205. 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 [2]. Lipoate-protein ligase A (LPLA) catalyses the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes [3]. The unusual biosynthesis pathway of lipoic acid is mechanistically intertwined with attachment of the cofactor [5].

Literature references

  1. 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

  2. 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

  3. 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

  4. Reche PA; , Protein Sci 2000;9:1922-1929.: Lipoylating and biotinylating enzymes contain a homologous catalytic module. PUBMED:11106165 EPMC:11106165

  5. Cronan JE, Zhao X, Jiang Y; , Adv Microb Physiol. 2005;50:103-146.: Function, attachment and synthesis of lipoic acid in Escherichia coli. PUBMED:16221579 EPMC:16221579


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004143

This domain is found in 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 [PUBMED:10470036]. Lipoate-protein ligase A (LPLA) (octanoyltransferase) catalyses the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes [PUBMED:8206909].

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan tRNA_synt_II (CL0040), which contains the following 9 members:

AsnA BPL_LplA_LipB DUF544 tRNA-synt_2 tRNA-synt_2b tRNA-synt_2c tRNA-synt_2d tRNA-synt_2e tRNA-synt_His

Alignments

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(4175)
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RP35
(1916)
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RP75
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  Seed
(66)
Full
(11826)
Representative proteomes NCBI
(8364)
Meta
(4175)
RP15
(1020)
RP35
(1916)
RP55
(2578)
RP75
(3031)
Alignment:
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  Seed
(66)
Full
(11826)
Representative proteomes NCBI
(8364)
Meta
(4175)
RP15
(1020)
RP35
(1916)
RP55
(2578)
RP75
(3031)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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Pfam alignments:

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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: Reche P
Previous IDs: BPL_LipA_LipB;
Type: Domain
Author: Bateman A, Reche P
Number in seed: 66
Number in full: 11826
Average length of the domain: 120.70 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 40.71 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 125
Family (HMM) version: 14
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Species distribution

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Interactions

There are 4 interactions for this family. More...

BPL_LplA_LipB Lip_prot_lig_C BPL_C HTH_11

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 domain has been found. There are 113 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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