title: Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants.
abstract: BACKGROUND
  Tryptophan synthase consists of two subunits, alpha and beta. Two distinct subgroups of beta chain exist. The major group (TrpEb_1) includes the well-studied beta chain of Salmonella typhimurium. The minor group of beta chain (TrpEb_2) is most frequently found in the Archaea. Most of the amino-acid residues important for catalysis are highly conserved between both TrpE subfamilies.
  
  
  RESULTS
  Conserved amino-acid residues of TrpEb_1 that make allosteric contact with the TrpEa subunit (the alpha chain) are absent in TrpEb_2. Representatives of Archaea, Bacteria and higher plants all exist that possess both TrpEb_1 and TrpEb_2. In those prokaryotes where two trpEb genes coexist, one is usually trpEb_1 and is adjacent to trpEa, whereas the second is trpEb_2 and is usually unlinked with other tryptophan-pathway genes.
  
  
  CONCLUSIONS
  TrpEb_1 is nearly always partnered with TrpEa in the tryptophan synthase reaction. However, by default at least six lineages of the Archaea are likely to use TrpEb_2 as the functional beta chain, as TrpEb_1 is absent. The six lineages show a distinctive divergence within the overall TrpEa phylogenetic tree, consistent with the lack of selection for amino-acid residues in TrpEa that are otherwise conserved for interfacing with TrpEb_1. We suggest that the standalone function of TrpEb_2 might be to catalyze the serine deaminase reaction, an established catalytic capability of tryptophan synthase beta chains. A coincident finding of interest is that the Archaea seem to use the citramalate pathway, rather than threonine deaminase (IlvA), to initiate the pathway of isoleucine biosynthesis.
authors.affiliation: BioScience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA. rjensen@ufl.edu
authors.forename: Gary
authors.initials: G
authors.lastname: Xie
authors.forename: Christian
authors.initials: C
authors.lastname: Forst
authors.forename: Carol
authors.initials: C
authors.lastname: Bonner
authors.forename: Roy A
authors.initials: RA
authors.lastname: Jensen
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000201:enzymology / Q000235:genetics*; D001419:Bacteria / Q000201:enzymology / Q000235:genetics*; D007527:Isoenzymes / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010944:Plants / Q000201:enzymology / Q000235:genetics*; D021122:Protein Subunits; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014367:Tryptophan Synthase / Q000235:genetics*
chemical_list: D007527:Isoenzymes; D021122:Protein Subunits; D014367:Tryptophan Synthase