Home LiteratureArticle Details
PMID: 17400742 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Re-citrate synthase from Clostridium kluyveri is phylogenetically related to homocitrate synthase and isopropylmalate synthase rather than to Si-citrate synthase.

Journal of bacteriology ·Vol. 189 ·No. 11 ·2007-06-00 ·Pages 4299-304

Li F, Hagemeier CH, Seedorf H, Gottschalk G, Thauer RK

Abstract

The synthesis of citrate from acetyl-coenzyme A and oxaloacetate is catalyzed in most organisms by a Si-citrate synthase, which is Si-face stereospecific with respect to C-2 of oxaloacetate. However, in Clostridium kluyveri and some other strictly anaerobic bacteria, the reaction is catalyzed by a Re-citrate synthase, whose primary structure has remained elusive. We report here that Re-citrate synthase from C. kluyveri is the product of a gene predicted to encode isopropylmalate synthase. C. kluyveri is also shown to contain a gene for Si-citrate synthase, which explains why cell extracts of the organism always exhibit some Si-citrate synthase activity.

MeSH Terms
2-Isopropylmalate Synthase/genetics,metabolism Citrate (si)-Synthase/genetics,metabolism Citrates/chemistry,metabolism Clostridium kluyveri/enzymology,genetics,metabolism Genome, Bacterial Molecular Structure Oxaloacetic Acid/chemistry,metabolism Oxo-Acid-Lyases/genetics,metabolism Phylogeny Stereoisomerism
Chemicals
Citrates Oxaloacetic Acid Citrate (si)-Synthase 2-Isopropylmalate Synthase homocitrate synthase Oxo-Acid-Lyases
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Li Fuli
Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany.
Hagemeier Christoph H
Seedorf Henning
Gottschalk Gerhard
Thauer Rudolf K
References (48)
48 references, click to expand
  1. Citrate synthase and 2-methylcitrate synthase: structural, functional and evolutionary relationships.
    Microbiology. 1998 Apr;144 ( Pt 4):929-35 PMID: 9579066
  2. Synthesis of glutamate and citrate by Clostridium kluyveri. A new type of citrate synthase.
    Biochemistry. 1966 Apr;5(4):1125-33 PMID: 5958189
  3. Partial purification and some properties of the (R)-citrate synthase from Clostridium acidi-urici.
    Eur J Biochem. 1969 Jan;7(2):301-6 PMID: 4974734
  4. Stereochemistry of the interconversions of citrate and acetate catalyzed by citrate synthase, adenosine triphosphate citrate lyase, and citrate lyase.
    Biochemistry. 1971 Jun 8;10(12):2267-72 PMID: 5165527
  5. Cleavage of structural proteins during the assembly of the head of bacteriophage T4.
    Nature. 1970 Aug 15;227(5259):680-5 PMID: 5432063
  6. Stereochemistry of si-citrate synthase and ATP-citrate-lyase reactions.
    Eur J Biochem. 1971 Dec;24(2):207-15 PMID: 5157292
  7. Crystal structure of LeuA from Mycobacterium tuberculosis, a key enzyme in leucine biosynthesis.
    Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8295-300 PMID: 15159544
  8. THE ABSOLUTE STEREOCHEMICAL COURSE OF CITRIC ACID BIOSYNTHESIS.
    Proc Natl Acad Sci U S A. 1963 Nov;50:981-8 PMID: 14082366
  9. Identification and characterization of phosphinothricin-tripeptide biosynthetic genes in Streptomyces viridochromogenes.
    Gene. 1992 Jun 15;115(1-2):127-32 PMID: 1612426
  10. Studies on the re-citrate synthase reaction.
    Eur J Biochem. 1972 Apr 24;26(4):455-61 PMID: 5025927
  11. Absolute configuration of alpha isopropylmalate and the mechanism of its conversion to beta isopropylmalate in the biosynthesis of leucine.
    Biochemistry. 1973 Aug 14;12(17):3346-50 PMID: 4270046
  12. Studies on the biosynthesis of bialaphos (SF-1293). 18. 2-phosphinomethylmalic acid synthase: a descendant of (R)-citrate synthase?
    J Antibiot (Tokyo). 1999 Oct;52(10):925-31 PMID: 10604765
  13. The alpha-aminoadipate pathway for lysine biosynthesis in fungi.
    Cell Biochem Biophys. 2006;46(1):43-64 PMID: 16943623
  14. Glutamate biosynthesis in anaerobic bacteria. I. The citrate pathways of glutamate synthesis in Clostridium kluyveri.
    Biochemistry. 1966 Apr;5(4):1113-8 PMID: 5958187
  15. Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit.
    EMBO J. 2004 Sep 15;23(18):3621-31 PMID: 15329673
  16. Crystal structure of 2-methylisocitrate lyase (PrpB) from Escherichia coli and modelling of its ligand bound active centre.
    J Mol Biol. 2003 May 2;328(3):609-21 PMID: 12706720
  17. Synthesis and configurational assay of asymmetric methyl groups.
    Eur J Biochem. 1970 May 1;14(1):1-13 PMID: 5447433
  18. Citric-acid cycle, 50 years on. Modifications and an alternative pathway in anaerobic bacteria.
    Eur J Biochem. 1988 Oct 1;176(3):497-508 PMID: 3049083
  19. Stereochemistry of the re-citrate-synthase reaction.
    Eur J Biochem. 1971 Dec;24(2):216-21 PMID: 5157293
  20. How nature deals with stereoisomers.
    Curr Opin Struct Biol. 1995 Dec;5(6):830-6 PMID: 8749373
  21. Purification and characterization of citrate synthase from Streptomyces hygroscopicus SF-1293 and comparison of its properties with those of 2-phosphinomethylmalic acid synthase.
    Agric Biol Chem. 1990 Feb;54(2):463-70 PMID: 1368511
  22. Glutamate biosynthesis in anaerobic bacteria. II. Stereospecificity of aconitase and citrate synthetase of Clostridium kluyveri.
    Biochemistry. 1966 Apr;5(4):1119-24 PMID: 5958188
  23. Structural basis for stereoselectivity in the (R)- and (S)-hydroxypropylthioethanesulfonate dehydrogenases.
    Biochemistry. 2006 Jul 25;45(29):8831-40 PMID: 16846226
  24. Carbon dioxide and acetate utilization by Clostridium kluyveri. III. A new path of glutamic acid synthesis.
    J Biol Chem. 1954 Aug;209(2):605-9 PMID: 13192113
  25. The N-terminal and C-terminal portions of NifV are encoded by two different genes in Clostridium pasteurianum.
    J Bacteriol. 1991 May;173(10):3041-6 PMID: 2022611
  26. The crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 A resolution,.
    Biochemistry. 1997 Aug 19;36(33):9983-94 PMID: 9254593
  27. The absolute configuration of homocitric acid (2-hydroxy-1,2,4-butanetricarboxylic acid), an intermediate in lysine biosynthesis.
    Biochemistry. 1966 Aug;5(8):2513-6 PMID: 5968558
  28. (R)-citramalate synthase in methanogenic archaea.
    J Bacteriol. 1999 Jan;181(1):331-3 PMID: 9864346
  29. Identification of the stereoisomeric configurations of methylcitric acid produced by si-citrate synthase and methylcitrate synthase using capillary gas chromatography-mass spectrometry.
    J Inherit Metab Dis. 1994;17(6):738-47 PMID: 7707698
  30. Mechanism of aconitase action. I. The hydrogen transfer reaction.
    J Biol Chem. 1967 Apr 25;242(8):1870-9 PMID: 6024777
  31. Interpretation of experiments on metabolic processes, using isotopic tracer elements.
    Nature. 1948 Dec 18;162(4129):963 PMID: 18225319
  32. Biosynthesis of the iron-molybdenum cofactor of nitrogenase.
    Biofactors. 1988 Oct;1(3):199-205 PMID: 3076773
  33. D- and L-6-hydroxynicotine oxidase, enantiozymes of Arthrobacter oxidans.
    Z Naturforsch B. 1972 Sep;27(9):1072-3 PMID: 4405081
  34. Synthesis of trimethyl (2S,3R)- and (2R,3R)-[2-2H1]-homocitrates and dimethyl (2S,3R)- and (2R,3R)-[2-2H1]-homocitrate lactones-an assay for the stereochemical outcome of the reaction catalysed both by homocitrate synthase and by the Nif-V protein.
    Org Biomol Chem. 2006 Feb 7;4(3):569-80 PMID: 16446817
  35. Reversal of the stereospecificity of the citrate synthase of Clostridium kluyveri by p-chloromercuribenzoate.
    Biochem Biophys Res Commun. 1969 Feb 7;34(3):271-6 PMID: 5767022
  36. Kinetic analysis of the effects of monovalent cations and divalent metals on the activity of Mycobacterium tuberculosis alpha-isopropylmalate synthase.
    Arch Biochem Biophys. 2006 Jul 15;451(2):141-8 PMID: 16684501
  37. Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected].
    Science. 1992 Jun 5;256(5062):1445-8 PMID: 1604320
  38. Alpha-isopropylmalate synthase from Salmonella typhimurium. Purification and properties.
    J Biol Chem. 1969 Apr 25;244(8):2218-25 PMID: 4976555
  39. Asymmetry and enzyme action.
    Science. 1976 Jul 9;193(4248):121-5 PMID: 935862
  40. Horizontal gene transfer involved in the convergent evolution of the plasmid-encoded enantioselective 6-hydroxynicotine oxidases.
    J Mol Evol. 1999 Feb;48(2):178-86 PMID: 9929386
  41. The stereospecificity of the citrate synthase in sulfate-reducing and photosynthetic bacteria.
    Eur J Biochem. 1968 Aug;5(3):346-51 PMID: 5680354
  42. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.
    Anal Biochem. 1976 May 7;72:248-54 PMID: 942051
  43. Presence and stereospecificity of citrate synthase in anaerobic bacteria.
    Biochemistry. 1967 Apr;6(4):1027-34 PMID: 6032450
  44. The stereospecificity of the (R)-citrates synthase in the presence of p-chloromercuribenzoate.
    Biochem Biophys Res Commun. 1969 Aug 22;36(5):802-8 PMID: 5808294
  45. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.
    Nat Biotechnol. 2004 May;22(5):554-9 PMID: 15077118
  46. Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria.
    Arch Microbiol. 1997 Nov;168(5):428-36 PMID: 9325432
  47. Crystal structures of two bacterial 3-hydroxy-3-methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM barrel metalloenzymes cleaving carbon-carbon bonds.
    J Biol Chem. 2006 Mar 17;281(11):7533-45 PMID: 16330546
  48. Confirmation of unusual stereochemistry of glutamate biosynthesis in clostridium kluyveri.
    FEBS Lett. 1968 Jul;1(1):74-76 PMID: 11945256
Article Info
Journal
Journal of bacteriology
Abbr.
J Bacteriol
ISSN
0021-9193
DOI
10.1128/JB.00198-07
Published
2007-06-00
Epub
2007-00-30
Pages
4299-304
Language
English
Region
United States
NLM ID
2985120R
PMCID
PMC1913417
Subset
IM
External Links
PubMed source DOI: 10.1128/JB.00198-07 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2