Homology of the NifS family of proteins to a new class of pyridoxal phosphate‐dependent enzymes

Iterative profile sequence analysis reveals a remote homology of peroxisomal serine‐pyruvate aminotransferases from mammals to the small subunit of soluble hydrogenases from cyanobacteria, an isopenicillin N epimerase, the NifS gene products from bacteria and yeast, and the phosphoserine aminotransferase family. All members of this new class whose function is known are pyridoxal phosphate‐dependent enzymes, yet they have distinct catalytic activities. Upon alignment, a lysine around position 200 remains invariant and is predicted to be the pyridoxal phosphate‐binding residue. Based on the detected homology, it is predicted that NifS has also a pyridoxal phosphate‐dependent serine (or related) aminotransferase function associated with nitrogen economy and/or protection during nitrogen fixation.

[1]  P. Christen,et al.  Homology of pyridoxal-5'-phosphate-dependent aminotransferases with the cobC (cobalamin synthesis), nifS (nitrogen fixation), pabC (p-aminobenzoate synthesis) and malY (abolishing endogenous induction of the maltose system) gene products. , 1993, European journal of biochemistry.

[2]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[3]  E. Milgrom,et al.  A novel progesterone-induced messenger RNA in rabbit and human endometria. Cloning and sequence analysis of the complementary DNA. , 1987, Biochemistry.

[4]  M. Gribskov,et al.  [9] Profile analysis , 1990 .

[5]  R. Haselkorn,et al.  Bacterial-type ferredoxin genes in the nitrogen fixation regions of the cyanobacterium Anabaena sp. strain PCC 7120 and Rhizobium meliloti , 1988, Journal of bacteriology.

[6]  T. Oda,et al.  Generation from a single gene of two mRNAs that encode the mitochondrial and peroxisomal serine:pyruvate aminotransferase of rat liver. , 1990, The Journal of biological chemistry.

[7]  R. Robson,et al.  Nucleotide sequence and genetic analysis of the Azotobacter chroococcum nifUSVWZM gene cluster, including a new gene (nifP) which encodes a serine acetyltransferase , 1991, Journal of bacteriology.

[8]  B. Miflin,et al.  The path of ammonia assimilation in the plant kingdom , 1976 .

[9]  S. Usui,et al.  Purification and properties of isopenicillin N epimerase from Streptomyces clavuligerus. , 1989, Biochimica et biophysica acta.

[10]  R. Burris,et al.  Physiological reactions of the reversible hydrogenase from anabaena 7120. , 1981, Plant physiology.

[11]  M. Winkler,et al.  Extensive homology between the Escherichia coli K-12 SerC(PdxF) aminotransferase and a protein encoded by a progesterone-induced mRNA in rabbit and human endometria. , 1989, Nucleic acids research.

[12]  C. Sander,et al.  Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.

[13]  P. O'Gaora,et al.  Cloning and characterisation of the serC and aroA genes of Yersinia enterocolitica, and construction of an aroA mutant. , 1989, Gene.

[14]  B. Dujon,et al.  The complete DNA sequence of yeast chromosome III , 1992, Nature.

[15]  J. Beynon,et al.  Comparative organization of nitrogen fixation-specific genes from Azotobacter vinelandii and Klebsiella pneumoniae: DNA sequence of the nifUSV genes , 1987, Journal of bacteriology.

[16]  R. Thorneley,et al.  Structure and function of nitrogenase. , 1979, Annual review of biochemistry.

[17]  M Gribskov,et al.  Translational initiation factors IF-1 and eIF-2 alpha share an RNA-binding motif with prokaryotic ribosomal protein S1 and polynucleotide phosphorylase. , 1992, Gene.

[18]  A. Bairoch.  PROSITE: a dictionary of sites and patterns in proteins. , 1991, Nucleic acids research.

[19]  L. Packer,et al.  An inducible hydrogenase in cyanobacteria enhances N2 fixation , 1977, FEBS letters.

[20]  R. Haselkorn,et al.  Nitrogen fixation (nif) genes of the cyanobacterium Anabaena species strain PCC 7120. The nifB-fdxN-nifS-nifU operon. , 1989, The Journal of biological chemistry.

[21]  A. Smit,et al.  Nucleotide sequence of the gene proposed to encode the small subunit of the soluble hydrogenase of the thermophilic unicellular cyanobacterium Synechococcus PCC 6716. , 1989, Nucleic acids research.

[22]  R. Setterquist,et al.  Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii , 1989, Journal of bacteriology.

[23]  Geoffrey D. Smith,et al.  Soluble hydrogenase of Anabaena cylindrica , 1990 .

[24]  J. Postgate,et al.  Oxygen and hydrogen in biological nitrogen fixation. , 1980, Annual review of microbiology.

[25]  T. White,et al.  Genes required for formation of the apoMoFe protein of Klebsiella pneumoniae nitrogenase in Escherichia coli. , 1990, The Journal of biological chemistry.

[26]  J. Devereux,et al.  A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..

[27]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[28]  N. G. Carr,et al.  The Biology of Cyanobacteria , 1982 .

[29]  A. D. McLachlan,et al.  Profile analysis: detection of distantly related proteins. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[30]  J. Coggins,et al.  The serC-aro A operon of Escherichia coli. A mixed function operon encoding enzymes from two different amino acid biosynthetic pathways. , 1986, The Biochemical journal.

[31]  F. Ausubel.  Regulation of nitrogen fixation genes , 1984, Cell.

[32]  H. Griffin.  Nucleotide sequence of the Salmonella serC gene. , 1990, Nucleic acids research.

[33]  R. Doolittle,et al.  Progressive sequence alignment as a prerequisitetto correct phylogenetic trees , 2007, Journal of Molecular Evolution.

[34]  W. Orme-Johnson.  Molecular basis of biological nitrogen fixation. , 1985, Annual review of biophysics and biophysical chemistry.

[35]  G. Eichele,et al.  Mechanism of action of aspartate aminotransferase proposed on the basis of its spatial structure. , 1984, Journal of molecular biology.

[36]  R. Haselkorn,et al.  Deletion of a 55-kilobase-pair DNA element from the chromosome during heterocyst differentiation of Anabaena sp. strain PCC 7120 , 1988, Journal of bacteriology.

[37]  James R. Miller,et al.  The beta-lactam biosynthesis genes for isopenicillin N epimerase and deacetoxycephalosporin C synthetase are expressed from a single transcript in Streptomyces clavuligerus , 1990, Journal of bacteriology.

[38]  T. Oda,et al.  Cloning and nucleotide sequence of cDNA encoding human liver serine-pyruvate aminotransferase. , 1990, European journal of biochemistry.

[39]  A. Bairoch,et al.  The SWISS-PROT protein sequence data bank. , 1991, Nucleic acids research.

[40]  Y. Suzuki,et al.  Nucleotide sequence of the cDNA encoding the precursor for mitochondrial serine:pyruvate aminotransferase of rat liver. , 1987, European journal of biochemistry.

[41]  M Gribskov,et al.  Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins. , 1986, Nucleic acids research.