Logo of prosciprotein sciencecshl presssubscriptionsetoc alertsthe protein societyjournal home
Protein Sci. Oct 2000; 9(10): 1922–1929.
PMCID: PMC2144473

Lipoylating and biotinylating enzymes contain a homologous catalytic module.


Biotin and lipoic acid moieties are the covalently attached coenzyme cofactors of several multicomponent enzyme complexes that catalyze key metabolic reactions. Attachment of these moieties to the biotinyl- and lipoyl-dependent enzymes is post-translationally catalyzed by specific biotinylating and lipoylating protein enzymes. In Escherichia coli, two different enzymes, LplA and LipB, catalyze independent pathways for the lipoylation of the relevant enzymes, whereas only one enzyme, the BirA protein, is responsible for all the biotinylation. Counterparts of the E. coli BirA, LplA, and LipB enzymes have been previously identified in many organisms, but homology among the three families has never been reported. Computational analysis based on PSI-BLAST profiles and secondary structure predictions indicates, however, that lipoylating and biotinylating enzymes are evolutionarily related protein families containing a homologous catalytic module. Sequence conservation among the three families is very poor, but a single lysine residue is strictly conserved in all of them, which, according to the available X-ray crystal structure of the E. coli BirA protein, is expected to contribute to the binding of lipoic acid in the LplA and LipB enzymes.

Full Text

The Full Text of this article is available as a PDF (3.5M).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. [PMC free article] [PubMed]
  • Artymiuk PJ, Rice DW, Poirrette AR, Willet P. A tale of two synthetases. Nat Struct Biol. 1994 Nov;1(11):758–760. [PubMed]
  • Barker DF, Campbell AM. Genetic and biochemical characterization of the birA gene and its product: evidence for a direct role of biotin holoenzyme synthetase in repression of the biotin operon in Escherichia coli. J Mol Biol. 1981 Mar 15;146(4):469–492. [PubMed]
  • Buoncristiani MR, Howard PK, Otsuka AJ. DNA-binding and enzymatic domains of the bifunctional biotin operon repressor (BirA) of Escherichia coli. Gene. 1986;44(2-3):255–261. [PubMed]
  • Chapman-Smith A, Cronan JE., Jr The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity. Trends Biochem Sci. 1999 Sep;24(9):359–363. [PubMed]
  • Cronan JE., Jr The E. coli bio operon: transcriptional repression by an essential protein modification enzyme. Cell. 1989 Aug 11;58(3):427–429. [PubMed]
  • Cusack S. Sequence, structure and evolutionary relationships between class 2 aminoacyl-tRNA synthetases: an update. Biochimie. 1993;75(12):1077–1081. [PubMed]
  • Cusack S, Berthet-Colominas C, Härtlein M, Nassar N, Leberman R. A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A. Nature. 1990 Sep 20;347(6290):249–255. [PubMed]
  • Firestine SM, Nixon AE, Benkovic SJ. Threading your way to protein function. Chem Biol. 1996 Oct;3(10):779–783. [PubMed]
  • Fujiwara K, Okamura-Ikeda K, Motokawa Y. Purification and characterization of lipoyl-AMP:N epsilon-lysine lipoyltransferase from bovine liver mitochondria. J Biol Chem. 1994 Jun 17;269(24):16605–16609. [PubMed]
  • Fujiwara K, Okamura-Ikeda K, Motokawa Y. Cloning and expression of a cDNA encoding bovine lipoyltransferase. J Biol Chem. 1997 Dec 19;272(51):31974–31978. [PubMed]
  • Fujiwara K, Suzuki M, Okumachi Y, Okamura-Ikeda K, Fujiwara T, Takahashi E, Motokawa Y. Molecular cloning, structural characterization and chromosomal localization of human lipoyltransferase gene. Eur J Biochem. 1999 Mar;260(3):761–767. [PubMed]
  • Green NM. Avidin. Adv Protein Chem. 1975;29:85–133. [PubMed]
  • Jordan SW, Cronan JE., Jr A new metabolic link. The acyl carrier protein of lipid synthesis donates lipoic acid to the pyruvate dehydrogenase complex in Escherichia coli and mitochondria. J Biol Chem. 1997 Jul 18;272(29):17903–17906. [PubMed]
  • Harmon FR. Purification of antibodies against biotin of lipoic acid-Sepharose. Anal Biochem. 1980 Mar 15;103(1):58–63. [PubMed]
  • Holm L. Unification of protein families. Curr Opin Struct Biol. 1998 Jun;8(3):372–379. [PubMed]
  • Holm L, Sander C. Mapping the protein universe. Science. 1996 Aug 2;273(5275):595–603. [PubMed]
  • Hughey R, Krogh A. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci. 1996 Apr;12(2):95–107. [PubMed]
  • Knowles JR. The mechanism of biotin-dependent enzymes. Annu Rev Biochem. 1989;58:195–221. [PubMed]
  • Merritt EA, Murphy ME. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):869–873. [PubMed]
  • Morris TW, Reed KE, Cronan JE., Jr 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. 1994 Jun 10;269(23):16091–16100. [PubMed]
  • Morris TW, Reed KE, Cronan JE., Jr Lipoic acid metabolism in Escherichia coli: the lplA and lipB genes define redundant pathways for ligation of lipoyl groups to apoprotein. J Bacteriol. 1995 Jan;177(1):1–10. [PMC free article] [PubMed]
  • Nakatsu T, Kato H, Oda J. Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase. Nat Struct Biol. 1998 Jan;5(1):15–19. [PubMed]
  • Park J, Teichmann SA, Hubbard T, Chothia C. Intermediate sequences increase the detection of homology between sequences. J Mol Biol. 1997 Oct 17;273(1):349–354. [PubMed]
  • Perham RN. Domains, motifs, and linkers in 2-oxo acid dehydrogenase multienzyme complexes: a paradigm in the design of a multifunctional protein. Biochemistry. 1991 Sep 3;30(35):8501–8512. [PubMed]
  • Perham RN, Reche PA. Swinging arms in multifunctional enzymes and the specificity of post-translational modification. Biochem Soc Trans. 1998 Aug;26(3):299–303. [PubMed]
  • Reche P, Perham RN. Structure and selectivity in post-translational modification: attaching the biotinyl-lysine and lipoyl-lysine swinging arms in multifunctional enzymes. EMBO J. 1999 May 17;18(10):2673–2682. [PMC free article] [PubMed]
  • Richards NG, Schuster SM. Mechanistic issues in asparagine synthetase catalysis. Adv Enzymol Relat Areas Mol Biol. 1998;72:145–198. [PubMed]
  • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993 Dec 5;234(3):779–815. [PubMed]
  • Tsunoda JN, Yasunobu KT. Mammalian lipoic acid activating enzyme. Arch Biochem Biophys. 1967 Feb;118(2):395–401. [PubMed]
  • Westhead DR, Slidel TW, Flores TP, Thornton JM. Protein structural topology: Automated analysis and diagrammatic representation. Protein Sci. 1999 Apr;8(4):897–904. [PMC free article] [PubMed]
  • Wilson KP, Shewchuk LM, Brennan RG, Otsuka AJ, Matthews BW. Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):9257–9261. [PMC free article] [PubMed]
  • Wood HG, Harmon FR, Wühr B, Hübner K, Lynen F. Comparison of the biotination of apotranscarboxylase and its aposubunits. Is assembly essential for biotination? J Biol Chem. 1980 Aug 10;255(15):7397–7409. [PubMed]
  • Yamamoto K, Sekine T. Effect of avidin binding to SH1 on the interface between subfragment-1 and F-actin. J Biochem. 1987 Feb;101(2):519–523. [PubMed]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...