Biotechnology Letters

, Volume 37, Issue 2, pp 417–427 | Cite as

Fatty acid synthesis enzyme clans

Original Research Paper


Ketoacyl reductases (KRs), hydroxyacyl dehydratases (HDs), and enoyl reductases (ERs) are part of the fatty acid/polyketide synthesis cycle. They are known as acyl dehydrogenases, enoyl hydratases, and hydroxyacyl dehydrogenases, respectively, when catalyzing their reverse reactions. Earlier, we classified these enzymes into four KR, eight HD, and five ER families by statistical criteria. Members of all four KR families and three ER families have Rossmann folds, while five HD family members have HotDog folds. This suggests that those proteins with the same folds in different families may be distantly related, and therefore in clans, even though their amino acid sequences may not be homologous. We have now defined two clans containing three of the four KR families and two of the eight HD families, using manual and statistical tests. One of the ER families is related to the KR clan.


Enoyl reductases Hydroxyacyl dehydratases Ketoacyl reductases Phylogeny 



Root mean square deviation


Percentage of amino acid residues in the shorter (reference) molecule to that of the longer molecule used to calculate RMSDs

Supplementary material

10529_2014_1687_MOESM1_ESM.docx (20 kb)
Supplementary material 1 (DOCX 19 kb)


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Mol Biol 215:403–410CrossRefGoogle Scholar
  2. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acid Res 28:235–242PubMedCentralPubMedCrossRefGoogle Scholar
  3. Cantu DC, Chen Y, Reilly PJ (2010) Thioesterases: a new perspective based on their primary and tertiary structures. Protein Sci 19:1281–1295PubMedCentralPubMedCrossRefGoogle Scholar
  4. Cantu DC, Chen Y, Lemons ML, Reilly PJ (2011) ThYme: a database for thioester-active enzymes. Nucleic Acid Res 39:D342–D346PubMedCentralPubMedCrossRefGoogle Scholar
  5. Cantu DC, Dai T, Beversdorf ZS, Reilly PJ (2012) Structural classification and properties of ketoacyl reductases, hydroxyacyl dehydratases and enoyl reductases. Protein Eng Des Sel 25:803–811PubMedCrossRefGoogle Scholar
  6. Carvalho CC, Phan NN, Chen Y, Reilly PJ (2014) Carbohydrate binding module clans. Submitted for publicationGoogle Scholar
  7. Chen Y, Kelly EE, Masluk RP, Nelson CL, Cantu DC, Reilly PJ (2011) Structural classification and properties of ketoacyl synthases. Protein Sci 20:1659–1667PubMedCentralPubMedCrossRefGoogle Scholar
  8. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637PubMedCrossRefGoogle Scholar
  9. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (2014) The Carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acid Res 42:D490–D495PubMedCentralPubMedCrossRefGoogle Scholar
  10. Schrödinger LLC (2014) Portland, OR.
  11. Shatsky M, Nussinov R, Wolfson HJ (2004) A method for simultaneous alignment of multiple protein structures. Protein Struct Funct Bioinf 56:143–156CrossRefGoogle Scholar
  12. The MathWorks, Natick, MA (2014)

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Ngoc N. Phan
    • 1
  • Yuen Keong Lee
    • 1
  • Peter J. Reilly
    • 1
  1. 1.Department of Chemical and Biological EngineeringIowa State UniversityAmesUSA

Personalised recommendations