Divergent evolution of a β/α‐barrel subclass: Detection of numerous phosphate‐binding sites by motif search

Abstract

Study of the most conserved region in many @/a-barrels, the phosphate-binding site, revealed a sequence motif in a few @/a-barrels with known tertiary structure, namely glycolate oxidase (COX), cytochrome b2 (Cyb2), tryptophan synthase a subunit (TrpA), and the indoleglycerolphosphate synthase (TrpC). Database searches identified this motif in numerous other enzyme families: (1) IMP dehydrogenase (IMPDH) and GMP reductase (GuaC); (2) phosphoribosylformimino-5-aminoimidazol carboxamide ribotide isomerase (HisA) and the cyclaseproducing D-erythro-imidazole-glycerolphosphate (HisF) of the histidine biosynthetic pathway; (3) dihydroorotate dehydrogenase (PyrD); (4) glutamate synthase (GltB); ( 5 ) ThiE and ThiG involved in the biosynthesis of thiamine as well as related proteins; (6) an uncharacterized open reading frame from Erwinia herbicola; and (7) a glycerol uptake operon antiterminator regulatory protein (GlpP). Secondary structure predictions of the different families mentioned above revealed an alternating order of @-strands and a-helices in agreement with a @/a-barrel-like topology. The putative phosphate-binding site is always found near the C-terminus of the enzymes, which are all at least about 200 amino acids long. This is compatible with its assumed location between strand 7 and helix 8. The identification of a significant motif in functionally diverse enzymes suggests a divergent evolution of at least a considerable fraction of @/a-barrels. In addition to the known accumulation of @/a-barrels in the tryptophan biosynthetic pathway, we observe clusters of these enzymes in histidille biosynthesis, purine metabolism, and apparently also in thiamine biosynthesis. The substrates are mostly heterocyclic compounds. Although the marginal sequence similarities do not allow a reconstruction of the barrel spreading, they support the idea of pathway evolution by gene duplication.

d-Ribulose 5-Phosphate 3-Epimerase: Functional and Structural Relationships to Members of the Ribulose-Phosphate Binding (β/α)8-Barrel Superfamily,

“…Three of the latter interactions, those associated with Gly 178, Gly 198, and Ser 199, are located in the commonly observed, conserved phosphate binding motif located at the ends of the seventh and eighth -strands in ( /R) 8 -barrel enzymes (21). The fourth, associated with Gly 146, is located on a loop that is inserted between the end of the sixth -strand and the beginning of the sixth R-helix.…”

An Enzymatic Atavist Revealed in Dual Pathways for Water Activation

“…Alternatively, the dyad may have been present in the ancestral IMPDH/GMPR, but was subsequently remodeled in the GMPR lineage; since the flap binds in the same site as NAD + , this scenario suggests that the ancestral IMPDH/GMPR was a hydrolase. While we cannot rule out the latter scenario, we note that IMPDH is a member of the FMN oxidoreductase superfamily of (β/α) 8 barrel proteins (unfortunately, none of these proteins is sufficiently similar to permit rooting of the tree) [ 38 – 40 ]. Therefore, it seems more likely that the ancestral enzyme was a promiscuous dehydrogenase, and the flap carrying the hydrolase activity was the later addition.…”

Invariant glycines and prolines flanking in loops the strand β2 of various (α/β)8‐barrel enzymes: A hidden homology?

“…Recently, a large group of (a/&-barrel enzymes covering several families of glycosyl hydrolases (for the classification of glycohydrolases, see Henrissat, 1991;Henrissat & Bairoch, 1993) that contain their catalytic glutamates on strands 04 and 07, has been revealed (Henrissat et al, 1995;Jenkins et al, 1995). However, no clear sequence evidence has been offered up to now that would suggest homology among the substantial part of the seemingly unrelated (a/@),-barrels except for the finding of two sequence regions spanning the phosphate binding site in eight (a/&-barrelS (Wilmanns et al, 1991;Bork et al, 1995). It is worth mentioning, however, that motif searches with the key sites of the common phosphate binding site match a region in the vitamin B12 binding site of adenosylcobalamin-dependent mutase that belongs to another protein fold (Rossman fold).…”