Functional analysis of the methylmalonyl-CoA epimerase from Caenorhabditis elegans

FEBS Journal

Volumn 272, Issue 6, 2005, Pages 1465-1477

  Kühnl, Jochen ^a   Bobik, Thomas ^b   Procter, James B ^c   Burmeister, Cora ^a   Höppner, Jana ^a   Wilde, Inga ^a   Lüersen, Kai ^a   Torda, Andrew E ^c   Walter, Rolf D ^a   Liebau, Eva ^a  

^a BERNHARD NOCHT INSTITUTE FOR TROPICAL MEDICINE   (Germany)

^b IOWA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF HAMBURG   (Germany)

Author keywords

Caenorhabditis elegans; Epimerase; Methylmalonyl CoA

Indexed keywords

AMINO ACID; COENZYME A; FATTY ACID; GREEN FLUORESCENT PROTEIN; LIGAND; METAL; METHYLMALONYL COENZYME A EPIMERASE; PROPIONYL COENZYME A; SUCCINYL COENZYME A; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CAENORHABDITIS ELEGANS; ENZYME ACTIVITY; ENZYME ANALYSIS; ESCHERICHIA COLI; GENE; GENE EXPRESSION; LIGAND BINDING; MCE 1 GENE; METAL BINDING; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATIVE STRESS; PHARYNX; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; SUBCUTANEOUS TISSUE;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BINDING SITES; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; CONSENSUS SEQUENCE; EXONS; HUMANS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; RACEMASES AND EPIMERASES; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

CAENORHABDITIS ELEGANS; ESCHERICHIA COLI; HYPODERRIS;

EID: 20144387333     PISSN: 1742464X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2005.04579.x     Document Type: Article

References (48)

1. Armstrong RN (2000) Mechanistic diversity in a metalloenzyme superfamily. Biochemistry 39, 13625-13632.
2. Babbitt PC & Gerlt JA (1997) Understanding enzyme superfamilies. J Biol Chem 272, 30591-30594.
3. Gerlt JA & Babbitt PC (2001) Divergent Evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct superfamilies. Annu Rev Biochem 70, 209-246.
4. Fenton WA & Rosenberg LE (1995) Disorders of propionate and methylmalonate metabolism. In The Metabolic and Molecular Bases of Inherited Disease, Vol. 2. (Scriver CR, Beaudet AL, Sly WS & Valle D, eds), pp. 1423-1449. McGraw-Hill, New York.
5. Brusque AM, Borba RR, Schuck PF, Dalcin KB, Ribeiro CA, Silva CG, Wannmacher CM, Dutra-Filho CS, Wyse AT, Briones P & Wajner M (2002) Inhibition of the mitochondrial respiratory chain complex activities in rat cerebral cortex by methylmalonic acid. Neurochem Int 40, 593-601.
6. Kolker S, Schwab M, Horster F, Sauer S, Hinz A, Wolf NI, Mayatepek E, Hoffmann GF, Smeitink JA & Okun JG (2003) Methylmalonic acid, a biochemical hallmark of methylmalonic acidurias but no inhibitor of mitochondrial respiratory chain. J Biol Chem 278, 47388-47393.
7. Bobik TA & Rasche ME (2001) Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements: implications for decoding the human genome. J Biol Chem 276, 37194-37198.
8. Dayem LC, Carney JR, Santi DV, Pfeifer BA, Khosla C & Kealey JT (2002) Metabolic engineering of a methylmalonyl-CoA mutase-epimerase pathway for complex polyketide biosynthesis in Escherichia coli. Biochemistry 41, 5193-5201.
9. Herter S, Busch A & Fuchs G (2002) L-Malyl-coenzyme A lyase/beta-methylmalyl-coenzyme A lyase from Chloroflexus aurantiacus, a bifunctional enzyme involved in autotrophic CO(2) fixation. J Bacteriol 184, 5999-6006.
10. Korotkova N, Chistoserdova L, Kuksa K & Lidstrom ME (2002) Glyoxylate regeneration pathway in the methylotroph Methylobacterium extorquens AM1. J Bacteriol 184, 1750-1758.
11. Pfeifer BA & Khosla C (2001) Biosynthesis of polyketides in heterologous hosts. Microbiol Mol Biol Rev 65, 106-118.
12. Watanabe K, Rude MA, Walsh CT & Khosla C (2003) Engineered biosynthesis of an ansamycin polyketide precursor in Escherichia coli. Proc Natl Acad Sci USA 100, 9774-9778.
13. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W & Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
14. Harris TW, Chen NS, Cunningham F, Tello-Ruiz M, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Chan J et al. (2004) WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res 32, D411-D417.
15. Harris TW, Lee R, Schwarz E, Bradnam K, Lawson D, Chen W, Blasier D, Kenny E, Cunningham F, Kishore R et al. (2003) WormBase: a cross-species database for comparative genomics. Nucleic Acids Res 31, 133-137.
16. Stein L, Mangone M, Schwarz E, Durbin R, Thierry-Mieg J, Spieth J & Sternberg P (2001) WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res 29, 82-86.
17. Claros MG & Vincens P (1996) MITOPROT: Prediction of mitochondrial targeting sequences. Institut für Humangenetik, Technische Universität, München and Institut für Humangenetik GSF, Forschungszentrum für Gesundheit und Umwelt, Neuherberg, http://ihg.gsf.de/ihg/mitoprot.html.
18. Claros MG & Vincens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241, 779-786.
19. McCarthy AA, Baker HM, Shewry SC, Patchett ML & Baker EN (2001) Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold. Structure 9, 637-646.
20. Bergdoll M, Eltis LD, Cameron AD, Dumas P & Bolin JT (1998) All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly. Protein Sci 1, 1661-1670.
21. Fuller JQ & Leadlay PF (1983) Proton transfer in methylmalonyl-CoA epimerase from Propionibacterium shermanii. The reaction of (2R)-methylmalonyl- CoA in tritiated water. Biochem J 213, 643-650.
22. Peters JP & Elliot JM (1984) Effects of cobalt or hydroxycobalamin supplementation on vitamin B-12 content and (S)-methylmalonyl-CoA mutase activity of tissue from cobalt-depleted sheep. J Nutr 114, 660-670.
23. Dobson CM, Wai T, Leclerc D, Wilson A, Wu X, Dore C, Hudson T, Rosenblatt DS & Gravel RA (2002) Identification of the gene responsible for the cblA complementation group of vitamin B12-responsive methylmalonic acidemia based on analysis of prokaryotic gene arrangements. Proc Natl Acad Sci USA 99, 15554-15559.
24. Korotkova N & Lidstrom ME (2004) MeaB is a component of the methylmalonyl-CoA mutase complex required for protection of the enzyme from inactivation. J Biol Chem 279, 13652-13658.
25. Leal NA, Park SD, Kima PE & Bobik TA (2003) Identification of the human and bovine ATP: Cob (I) alamin adenosyltransferase cDNAs based on complementation of a bacterial mutant. J Biol Chem 278, 9227-9234.
26. Dobson CM, Wai T, Leclerc D, Kadir H, Narang M, Lerner-Ellis JP, Hudson TJ, Rosenblatt DS & Gravel RA (2002) Identification of the gene responsible for the cblB complementation group of vitamin B12-dependent methylmalonic aciduria. Hum Mol Genet 11, 3361-3369.
27. Kovachy RJ, Copley SD & Allen RH (1983) Recognition, isolation, and characterization of rat liver D-methylmalonyl coenzyme A hydrolase. J Biol Chem 258, 11415-11421.
28. Reszko AE, Kasumov T, Pierce BA, David F, Hoppel CL, Stanley WC, Des Rosiers C & Brunengraber H (2003) Assessing the reversibility of the anaplerotic reactions of the propionyl-CoA pathway in heart and liver. J Biol Chem 278, 34959-34965.
29. Montgomery JA, Mamer OA & Scriver CR (1983) Metabolism of methylmalonic acid in rats. Is methylmalonyl-coenzyme a racemase deficiency symptomatic in man? J Clin Invest 72, 1937-1947.
30. Mazumder R, Sasakawa T, Kaziro Y & Ochoa S (1962) Metabolism of propionic acid in animal tissues. IX. Methylmalonyl coenzyme A racemase. J Biol Chem 237, 3065-3068.
31. Wajner M, Latini A, Wyse AT & Dutra-Filho CS (2004) The role of oxidative damage in the neuropathology of organic acidurias: insights from animal studies. J Inherit Metab Dis 21, 427-434.
32. Fontella FU, Pulrolnik V, Gassen E, Wannmacher CM, Klein AB, Wajner M & Dutra-Filho CS (2000) Propionic and 1-methylmalonic acids induce oxidative stress in brain of young rats. Neuroreport 11, 541-544.
33. Lee SS, Lee RY, Fraser AG, Kamath RS, Ahringer J & Ruvkun G (2003) A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat Genet 33, 40-48.
34. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC & Ferrin TE (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25, 1605-1612.
35. Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, Fariselli P, Casadio R & Ben-Tal N (2004) ConSeq: The Identification of functionally and structurally important residues in protein sequences. Bioinformatics 20, 1322-1324.
36. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792-1797.
37. Higgins DG, Thompson JD & Gibson TJ (1996) Using CLUSTAL for multiple sequence alignments. Methods Enzymol 266, 383-402.
38. Gouy M (2004) Unrooted. http://pbil.University-lyon1.fr/software/ unrooted.html
39. Torda AE, Procter JB & Huber T (2004) Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. Nucleic Acids Res 32, W532-W535.
40. Fiser A & Sali A (2003) Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374, 461-491.
41. Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8, 52-56.
42. Hooft RWW, Vriend G, Sander C & Abola EE (1996) Errors in protein structures. Nature 381, 272-272.
43. Luthy R, Bowie JU & Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356, 83-85.
44. Clos J & Brandau S (1994) pJC20 and pJC40 - two high-copy-number vectors for T7 RNA polymerase-dependent expression of recombinant genes in Escherichia coli. Protein Expr Purif 5, 133-137.
45. Mello C & Fire A (1995) DNA transformation. Methods Cell Biol 48, 451-482.
46. Granato M, Schnabel H & Schnabel R (1994) Pha-1, a selectable marker for gene transfer in C. elegans. Nucleic Acids Res 22, 1762-1763.
47. Timmons L & Fire A (2001) Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 263, 103-112.
48. Jansen G, Hazendonk E, Thijssen KL & Plasterk RH (1997) Reverse genetics by chemical mutagenesis in Caenorhabditis elegans. Nat Genet 17, 119-121.