The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (β/α)₈barrel enzymes

Abstract

The IMPDH/GMPR family of (β/α)8 enzymes presents an excellent opportunity to investigate how subtle changes in enzyme structure change reaction specificity. IMP dehydrogenase (IMPDH) and GMP reductase (GMPR) bind the same ligands with similar affinities and share a common set of catalytic residues. Both enzymes catalyze a hydride transfer reaction involving a nicotinamide cofactor hydride, and both reactions proceed via the same covalent intermediate. In the case of IMPDH, this intermediate reacts with water while in GMPR it reacts with ammonia. In both cases, the two chemical transformations are separated by a conformational change. In IMPDH, the conformational change involves a mobile protein flap while in GMPR the cofactor moves. Thus reaction specificity is controlled by differences in dynamics, which in turn are controlled by residues outside the active site. These findings have some intriguing implications for the evolution of the IMPDH/GMPR family.

The cystathionine‐β‐synthase domains on the guanosine 5′’‐monophosphate reductase and inosine 5′‐monophosphate dehydrogenase enzymes from Leishmania regulate enzymatic activity in response to guanylate and adenylate nucleotide levels

“…Bioinformatic and structural comparisons with the Tritrichomonas foetus IMPDH and human GMPR (Patton et al ., ; Prosise and Luecke, ) permitted the identification of a number of functional motifs in LmGMPR. These include: (i) the highly conserved IMPDH/GMPR signature sequence containing an active site catalytic cysteine that forms an enzyme‐XMP or enzyme‐IMP covalent intermediate (Hedstrom, ; Gan et al ., ), (ii) an NADPH‐binding site that predominantly forms interactions with the adenine moiety of the cofactor, (iii) an IMP/GMP binding cassette that forms contacts with the ribose‐5′‐phosphate, or the 6‐exocyclic oxygen constituent of the nucleotide substrate, (iv) a low‐affinity mycophenolic acid binding motif and (v) a C‐terminal tripeptide (Ser‐Lys‐Leu), a type 1 topogenic signal that targets proteins to the glycosome (Riera et al ., ; Dobie et al ., ; Gan et al ., ; Jardim et al ., ; Umejiego et al ., ; Zarella‐Boitz et al ., ; Sintchak et al ., ), a peroxisomal‐like microbody present in Leishmania and related trypanosomatids (Michels et al ., ) (Fig. ).…”

Allosteric regulation accompanied by oligomeric state changes of Trypanosoma brucei GMP reductase through cystathionine-β-synthase domain

“…In terms of the structures, TbGMPR shows very high homologies to IMPDHs, a (β/α) 8 barrel protein also composed of catalytic and CBS domains 7 . The activity regulation of IMPDHs is accompanied by their conformational changes, and the relationship between the activity and the conformation is extensively investigated to date 14,15,17 .…”

“…None None GTP GTP GMP GMP ATP ATP 7 8 or guanine nucleotides to the allosteric regulatory site. The GMPR of T. brucei is distinguishable from those of the host animals by the presence of CBS domain 6,9 ; therefore, the CBS domain might be a good therapeutic target for African trypanosomiasis.…”

“…Our previous studies have demonstrated that a purine nucleotide analog, ribavirin 5ʹ-monophosphate, acts as an inhibitor for both T. brucei GMPR (TbGMPR) and IMPDH (TbIMPDH), but also shows an anti-trypanosomal effect in culture when provided in the nucleoside form, ribavirin 5,6 . In general, both GMPRs and IMPDHs have strong similarities in amino acid sequence, and their catalytic domains share the common structure of a (β/α) 8 barrel, also referred to as a TIM barrel 7 ; nevertheless, these two enzymes are still distinctive each other by the presence or absence of an additional domain 8 . This additional domain is known as a cystathionine-β-synthase (CBS) or Bateman domain that consists of a tandem repeat of α-β-β-α folds, and is found in IMPDHs of all organisms reported to date.…”

Molecular Mechanisms of Enzyme Activation by Monovalent Cations

“…M ϩ complexation also propagates entropic benefits to the entire structure of the enzyme by selecting more ordered and catalytically active conformations from an ensemble dominated by disordered and poorly active conformers. This is documented in clotting proteases (16,17), inosine monophosphate dehydrogenase (18), several ␣-amylases (19 -21), and kinases (22,23), and is a determining factor of ion selectivity in the Streptomyces lividans K ϩ channel (10). ATPdriven sequential switching between Na ϩ -specific and K ϩ -specific conformations drives ion transport in the Na/K-ATPase (11,24).…”