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28  structures 1410  species 0  interactions 1760  sequences 12  architectures

Family: Lip_prot_lig_C (PF10437)

Summary: Bacterial lipoate protein ligase C-terminus

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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]
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
Biotin protein ligase C terminal domain
Pfam clanCL0206

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]


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]


  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. doi:10.1016/s0968-0004(99)01438-3. 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. Advances in Microbial Physiology. 50. pp. 103–46. doi:10.1016/S0065-2911(05)50003-1. ISBN 9780120277506. 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.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Bacterial lipoate protein ligase C-terminus Provide feedback

This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C-terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with the domain BPL_LipA_LipB PF03099 further upstream. This domain is required for adenylation of lipoic acid by lipoate protein ligases. The domain is not required for transfer of lipoic acid from the adenylate to the lipoyl domain. Upon adenylation, this domain rotates 180 degrees away from the active site cleft. Therefore, the domain does not interact with the lipoyl domain during transfer.

Literature references

  1. McManus E, Luisi BF, Perham RN; , J Mol Biol. 2006;356:625-637.: Structure of a putative lipoate protein ligase from Thermoplasma acidophilum and the mechanism of target selection for post-translational modification. PUBMED:16384580 EPMC:16384580

  2. Christensen QH, Cronan JE;, J Biol Chem. 2009;284:21317-21326.: The Thermoplasma acidophilum LplA-LplB complex defines a new class of bipartite lipoate-protein ligases. PUBMED:19520844 EPMC:19520844

  3. Fujiwara K, Maita N, Hosaka H, Okamura-Ikeda K, Nakagawa A, Taniguchi H;, J Biol Chem. 2010;285:9971-9980.: Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A. PUBMED:20089862 EPMC:20089862

This tab holds annotation information from the InterPro database.

InterPro entry IPR019491

This is the C-terminal domain of a bacterial lipoate protein ligase [ PUBMED:16043486 ]. There is no conservation between this C terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with INTERPRO , further upstream. This C-terminal domain is more stable than INTERPRO and the hypothesis is that the C-terminal domain has a role in recognising the lipoyl domain and/or transferring the lipoyl group onto it from the lipoyl-AMP intermediate. C-terminal fragments of length 172 to 193 amino acid residues are observed in the eubacterial enzymes whereas in their archaeal counterparts the C-terminal segment is significantly smaller, ranging in size from 87 to 107 amino acid residues.

Domain organisation

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Pfam Clan

This family is a member of clan SufE_NifU (CL0233), which has the following description:

This clan includes iron sulfur cluster assembly proteins.

The clan contains the following 4 members:

CO_deh_flav_C Lip_prot_lig_C NifU_N SufE


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Curation and family details

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Seed source: Gene3D, pdb_1vqz
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Coggill P
Number in seed: 205
Number in full: 1760
Average length of the domain: 84.20 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 25.42 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 85
Family (HMM) version: 11
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Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 Lip_prot_lig_C domain has been found. There are 28 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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