Alpha-methylacyl-CoA racemase

Alpha-methylacyl-CoA racemase

alpha-methylacyl-CoA racemase
EC number
CAS number 156681-44-6
IntEnz IntEnz view
ExPASy NiceZyme view
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO

In enzymology, an alpha-methylacyl-CoA racemase also known as AMACR is an enzyme that catalyzes the chemical reaction

(2R)-2-methylacyl-CoA \rightleftharpoons (2S)-2-methylacyl-CoA

In mammalian cells, the enzyme is responsible for converting (2R)-methylacyl-CoA esters to their (2S)-methylacyl-CoA epimers and known substrates include coenzyme A esters of pristanic acid (mostly derived from phytanic acid, a 3-methyl branched-chain fatty acid that is abundant in the diet) and bile acids derived from cholesterol. This transformation is required in order to degrade (2R)-methylacyl-CoA esters by β-oxidation, which requires the (2S) epimer. The enzyme is known to be localised in peroxisomes and mitochondria, both of which are known to β-oxidise 2-methylacyl-CoA esters.[1][2]


This enzyme belongs to the family of isomerases, to be specific those racemases and epimerases acting on other compounds. The systematic name of this enzyme class is 2-methylacyl-CoA 2-epimerase. In vitro experiments with the human enzyme AMACR 1A show that both (2S)- and (2R)-methyldecanoyl-CoA esters are substrates and are converted by the enzyme with very similar efficiency. Prolonged incubation of either substrate with the enzyme establishes an equilibrium with both substrates/products present in a near 1:1 ratio. The mechanism of the enzyme requires removal of the α-proton of the 2-methylacyl-CoA to form a deprotonated intermediate [which is probably the enol or enolate[3] followed by non-sterespecific reprotonation.[4] Thus either epimer is converted into a near 1:1 mixture of both isomers upon full conversion of substrate.


Alpha-methylacyl-CoA racemase
Symbols  ; AMACRD; CBAS4; RACE; RM
External IDs GeneCards:
EC number
Species Human Mouse
RefSeq (mRNA)
RefSeq (protein)
Location (UCSC)
PubMed search

Alpha-methylacyl-CoA racemase in humans is encoded by the AMACR gene.[5][6][7]

Protein structure

As of late 2007, 7 structures have been solved for this class of enzymes, with PDB accession codes 1X74, 2G04, 2GCE, 2GCI, 2GD0, 2GD2, and 2GD6. A structure of the proposed deprotonated intermediate has since been published.[3] These structures are of the Mycobacterium tuberculosis version of the enzyme, known as MCR.

Clinical significance

Both decreased and increased levels of the enzyme in humans is linked with diseases.

Neurological diseases

Reduction of protein levels or activity results in the accumulation of (2R)-methyl fatty acids such as bile acids which results in neurological symptoms. The symptoms are similar to adult Refsum disease and usually appear in the late teens or early 20's.[8]

AMACR deficiency has recently been discovered. The first documented case was in 2006. It is in a class of disorders called peroxisome biogenesis disorders (PBD) although it is quite different than other peroxisomal disorders and does not share classic Refsum disorder symptoms. It causes an accumulation of pristanic acid, DHCA and EHCA and to a lesser extent VLCFA and phytanic acid. "His condition would have been missed if they hadn't measured the pristanic acid concentration." [9]

It can cause mental impairment,confusion, learning difficulties and liver damage. It can be treated by dietary elimination of pristanic and phytanic acid from meats such as beef, lamb, chicken, and dairy products, however compliance to the diet is low due to dietary habits, and loss of weight.[10][11]


Increased levels of AMACR protein and activity are associated with prostate cancer, and the enzyme is used widely as a biomarker (known in the cancer literature as P504S) in biopsy tissues. Around 10 different variants of human AMACR have been identified from prostate cancer tissues, which arise from alternative mRNA splicing. Some of these splice variants lack catalytic residues in the active site or have changes in the C-terminus which is required for dimerisation. Increased levels of AMACR are also associated with some breast, colon and other cancers but it is unclear exactly what the role of AMACR is in these cancers.[2][12][13]

Antibodies to AMACR are used in immunohistochemistry to demonstrate prostate carcinoma, since the enzyme is greatly over-expressed in this type of tumour.[14]

Ibuprofen metabolism

The enzyme is also involved in a chiral inversion pathway which converts ibuprofen, a member of the 2-arylpropionic acid (2-APA) of the non-steroidal anti-inflammatory drug family (NSAIDs) from the R-enantiomer to the S-enantiomer. The pathway is uni-directional because only R-ibuprofen can be converted into ibuprofenoyl-CoA, which is then epimerised by AMACR. Conversion of S-ibuprofenoyl-CoA to S-ibuprofen is assumed to be performed by one of the many human acyl-CoA thioesterase enzymes (ACOTs). The reaction is of pharmacological importance because ibuprofen is typically used as a racemic mixture, and the drug is converted to the S-isomer upon uptake, which inhibit the activity of the cyclo-oxygenase enzymes and hence bring about an anti-inflammatory effect. Recently human AMACR 1A has been demonstrated to epimerise other 2-APA-CoA esters,[15] suggesting a common chiral inversion pathway for this class of drugs.


  1. ^ Schmitz W, Fingerhut R, Conzelmann E (June 1994). "Purification and properties of an alpha-methylacyl-CoA racemase from rat liver". Eur. J. Biochem. 222 (2): 313–23. PMID 8020470. doi:10.1111/j.1432-1033.1994.tb18870.x. 
  2. ^ a b Lloyd MD, Darley DJ, Wierzbicki AS, Threadgill MD (March 2008). "Alpha-methylacyl-CoA racemase--an 'obscure' metabolic enzyme takes centre stage". FEBS J. 275 (6): 1089–102. PMID 18279392. doi:10.1111/j.1742-4658.2008.06290.x. 
  3. ^ a b Sharma S, Bhaumik P, Schmitz W, Venkatesan R, Hiltunen JK, Conzelmann E, Juffer AH, Wierenga RK (March 2012). "The enolization chemistry of a thioester-dependent racemase: the 1.4 Å crystal structure of a reaction intermediate complex characterized by detailed QM/MM calculations". J Phys Chem B 116 (11): 3619–29. PMID 22360758. doi:10.1021/jp210185m. 
  4. ^ Darley DJ, Butler DS, Prideaux SJ, Thornton TW, Wilson AD, Woodman TJ, Threadgill MD, Lloyd MD (February 2009). "Synthesis and use of isotope-labelled substrates for a mechanistic study on human alpha-methylacyl-CoA racemase 1A (AMACR; P504S)". Org. Biomol. Chem. 7 (3): 543–52. PMID 19156321. doi:10.1039/b815396e. 
  5. ^ "Entrez Gene: AMACR alpha-methylacyl-CoA racemase". 
  6. ^ Schmitz W, Helander HM, Hiltunen JK, Conzelmann E (September 1997). "Molecular cloning of cDNA species for rat and mouse liver alpha-methylacyl-CoA racemases". Biochem. J. 326. ( Pt 3): 883–9. PMC 1218746. PMID 9307041. 
  7. ^ "P504S, a-methylacyl-CoA racemase, AMACR". Retrieved 25 April 2012. 
  8. ^ Ferdinandusse S, Denis S, Clayton PT, Graham A, Rees JE, Allen JT, McLean BN, Brown AY, Vreken P, Waterham HR, Wanders RJ (February 2000). "Mutations in the gene encoding peroxisomal alpha-methylacyl-CoA racemase cause adult-onset sensory motor neuropathy". Nat. Genet. 24 (2): 188–91. PMID 10655068. doi:10.1038/72861. 
  9. ^ McLean BN, Allen J, Ferdinandusse S, Wanders RJ (March 2002). "A new defect of peroxisomal function involving pristanic acid: a case report". J. Neurol. Neurosurg. Psychiatr. 72 (3): 396–9. PMC 1737782. PMID 11861706. doi:10.1136/jnnp.72.3.396. 
  10. ^ Chedrawi A, Clark GD (2007-03-08). "Peroxisomal Disorders: Overview - eMedicine Neurology". Archived from the original on 2 March 2009. Retrieved 2009-03-16. 
  11. ^ Wanders RJA, Waterham HR, Leroy BP (2006-03-20). "Refsum Disease". GeneReviews -- NCBI Bookshelf. Retrieved 2009-03-16. 
  12. ^ Ouyang B, Leung YK, Wang V, Chung E, Levin L, Bracken B, Cheng L, Ho SM (January 2011). "α-Methylacyl-CoA racemase spliced variants and their expression in normal and malignant prostate tissues". Urology 77 (1): 249.e1–7. PMC 3051191. PMID 21195844. doi:10.1016/j.urology.2010.08.005. 
  13. ^ Rubin MA, Bismar TA, Andrén O, Mucci L, Kim R, Shen R, Ghosh D, Wei JT, Chinnaiyan AM, Adami HO, Kantoff PW, Johansson JE (June 2005). "Decreased alpha-methylacyl CoA racemase expression in localized prostate cancer is associated with an increased rate of biochemical recurrence and cancer-specific death". Cancer Epidemiol. Biomarkers Prev. 14 (6): 1424–32. PMID 15941951. doi:10.1158/1055-9965.EPI-04-0801. 
  14. ^ Zhou, M. et al. (2003). "Expression and diagnostic utility of alpha-methylacyl-CoA-racemase (P504S) in foamy gland and pseudohyperplastic prostate cancer". American Journal of Surgical Pathology 27 (6): 772–778. doi:10.1097/00000478-200306000-00007. 
  15. ^ Woodman TJ, Wood PJ, Thompson AS, Hutchings TJ, Steel GR, Jiao P, Threadgill MD, Lloyd MD (July 2011). "Chiral inversion of 2-arylpropionyl-CoA esters by human α-methylacyl-CoA racemase 1A (P504S)—a potential mechanism for the anti-cancer effects of ibuprofen". Chem. Commun. (Camb.) 47 (26): 7332–4. PMID 21614403. doi:10.1039/c1cc10763a. 

Further reading

  • Jiang Z, Woda BA, Wu CL, Yang XJ (2004). "Discovery and clinical application of a novel prostate cancer marker: alpha-methylacyl CoA racemase (P504S).". Am. J. Clin. Pathol. 122 (2): 275–89. PMID 15323145. doi:10.1309/EJUY-UQPE-X1MG-68MK. 
  • Bautch S (1991). "Wisconsin doctor selected as national symbol of physicians' sacrifices.". Wis. Med. J. 90 (8): 485–7. PMID 1926890. 
  • Schmitz W, Albers C, Fingerhut R, Conzelmann E (1995). "Purification and characterization of an alpha-methylacyl-CoA racemase from human liver.". Eur. J. Biochem. 231 (3): 815–22. PMID 7649182. doi:10.1111/j.1432-1033.1995.tb20766.x. 
  • Maruyama K, Sugano S (1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides.". Gene 138 (1-2): 171–4. PMID 8125298. doi:10.1016/0378-1119(94)90802-8. 
  • Schmitz W, Helander HM, Hiltunen JK, Conzelmann E (1997). "Molecular cloning of cDNA species for rat and mouse liver alpha-methylacyl-CoA racemases.". Biochem. J. 326. ( Pt 3): 883–9. PMC 1218746. PMID 9307041. 
  • Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, et al. (1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library.". Gene 200 (1-2): 149–56. PMID 9373149. doi:10.1016/S0378-1119(97)00411-3. 
  • Ferdinandusse S, Denis S, Clayton PT, et al. (2000). "Mutations in the gene encoding peroxisomal alpha-methylacyl-CoA racemase cause adult-onset sensory motor neuropathy.". Nat. Genet. 24 (2): 188–91. PMID 10655068. doi:10.1038/72861. 
  • Kotti TJ, Savolainen K, Helander HM, et al. (2000). "In mouse alpha -methylacyl-CoA racemase, the same gene product is simultaneously located in mitochondria and peroxisomes.". J. Biol. Chem. 275 (27): 20887–95. PMID 10770938. doi:10.1074/jbc.M002067200. 
  • Amery L, Fransen M, De Nys K, et al. (2001). "Mitochondrial and peroxisomal targeting of 2-methylacyl-CoA racemase in humans.". J. Lipid Res. 41 (11): 1752–9. PMID 11060344. 
  • Hartley JL, Temple GF, Brasch MA (2001). "DNA cloning using in vitro site-specific recombination.". Genome Res. 10 (11): 1788–95. PMC 310948. PMID 11076863. doi:10.1101/gr.143000. 
  • Rubin MA, Zhou M, Dhanasekaran SM, et al. (2002). "alpha-Methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer.". JAMA 287 (13): 1662–70. PMID 11926890. doi:10.1001/jama.287.13.1662. 
  • Luo J, Zha S, Gage WR, et al. (2002). "Alpha-methylacyl-CoA racemase: a new molecular marker for prostate cancer.". Cancer Res. 62 (8): 2220–6. PMID 11956072. 
  • Zhou M, Chinnaiyan AM, Kleer CG, et al. (2002). "Alpha-Methylacyl-CoA racemase: a novel tumor marker over-expressed in several human cancers and their precursor lesions.". Am. J. Surg. Pathol. 26 (7): 926–31. PMID 12131161. doi:10.1097/00000478-200207000-00012. 
  • Kuefer R, Varambally S, Zhou M, et al. (2002). "alpha-Methylacyl-CoA racemase: expression levels of this novel cancer biomarker depend on tumor differentiation.". Am. J. Pathol. 161 (3): 841–8. PMC 1867250. PMID 12213712. doi:10.1016/S0002-9440(10)64244-7. 
  • Varambally S, Dhanasekaran SM, Zhou M, et al. (2002). "The polycomb group protein EZH2 is involved in progression of prostate cancer.". Nature 419 (6907): 624–9. PMID 12374981. doi:10.1038/nature01075. 
  • Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. PMC 139241. PMID 12477932. doi:10.1073/pnas.242603899. 
  • Leav I, McNeal JE, Ho SM, Jiang Z (2003). "Alpha-methylacyl-CoA racemase (P504S) expression in evolving carcinomas within benign prostatic hyperplasia and in cancers of the transition zone.". Hum. Pathol. 34 (3): 228–33. PMID 12673556. doi:10.1053/hupa.2003.42. 
  • Shen-Ong GL, Feng Y, Troyer DA (2003). "Expression profiling identifies a novel alpha-methylacyl-CoA racemase exon with fumarate hydratase homology.". Cancer Res. 63 (12): 3296–301. PMID 12810662. 
  • Zha S, Ferdinandusse S, Denis S, et al. (2004). "Alpha-methylacyl-CoA racemase as an androgen-independent growth modifier in prostate cancer.". Cancer Res. 63 (21): 7365–76. PMID 14612535. 
  • Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs.". Nat. Genet. 36 (1): 40–5. PMID 14702039. doi:10.1038/ng1285.