scholarly journals Design of potential bisubstrate inhibitors against Mycobacterium tuberculosis (Mtb) 1-deoxy-d-xylulose 5-phosphate reductoisomerase (Dxr)—evidence of a novel binding mode

MedChemComm ◽  
2013 ◽  
Vol 4 (7) ◽  
pp. 1099 ◽  
Author(s):  
Géraldine San Jose ◽  
Emily R. Jackson ◽  
Eugene Uh ◽  
Chinchu Johny ◽  
Amanda Haymond ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Binding Mode ◽  
Bisubstrate Inhibitors

Bisubstrate Inhibitors for the Enzyme Catechol O-Methyltransferase (COMT): Dramatic Effects of Ribose Modifications on Binding Affinity and Binding Mode

2003 ◽  
Vol 86 (4) ◽  
pp. 1045-1062 ◽  
Author(s):  
Christian Lerner ◽  
Romain Siegrist ◽  
Eliane Schweizer ◽  
François Diederich ◽  
Volker Gramlich ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Binding Mode ◽  
Bisubstrate Inhibitors

NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase–NAD complex

2005 ◽  
Vol 327 (2) ◽  
pp. 500-508 ◽  
Author(s):  
Shigetarou Mori ◽  
Masayuki Yamasaki ◽  
Yukie Maruyama ◽  
Keiko Momma ◽  
Shigeyuki Kawai ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
Binding Mode ◽  
Nad Kinase

scholarly journals Characterization of coenzyme binding and selectivity determinants in Mycobacterium tuberculosis flavoprotein reductase A: analysis of Arg199 and Arg200 mutants at the NADP(H) 2′-phosphate binding site

2008 ◽  
Vol 417 (1) ◽  
pp. 103-114 ◽  
Author(s):  
Muna Sabri ◽  
Adrian J. Dunford ◽  
Kirsty J. McLean ◽  
Rajasekhar Neeli ◽  
Nigel S. Scrutton ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Substrate Inhibition ◽  
Reduction Rate ◽  
Binding Mode ◽  
Phosphate Binding ◽  
Ferricyanide Reduction ◽  
Coenzyme Specificity ◽  
Coenzyme Binding ◽  
Kd Values ◽  
Adrenodoxin Reductase

Mycobacterium tuberculosis FprA (flavoprotein reductase A) is an NAD(P)H- and FAD-binding reductase that is structurally/evolutionarily related to adrenodoxin reductase. Structural analysis implicates Arg199 and Arg200 in interactions with the NADP(H) 2′-phosphate group. R199A, R200A and R199A/R200A mutants were characterized to explore the roles of these basic residues. All mutations abolished neutral FAD semiquinone stabilization in the NADPH-reduced enzyme, owing to weakened NADPH affinity. Instead, FAD hydroquinone was formed in all mutants, and each displayed substantially enhanced autooxidation rates (20–40-fold) compared with NADPH-reduced WT (wild-type) FprA. Steady-state ferricyanide reduction studies revealed diminished NADPH affinity (higher Km values), but lower NADH Km values. Despite a lowered kcat, the R199A/R200A mutant exhibited a 200-fold coenzyme specificity switch towards NADH, although substrate inhibition was observed at high NADH concentrations (Ki=250 μM). Stopped-flow FAD reduction studies confirmed substantially increased NADPH Kd values, although the limiting flavin reduction rate constant was similar in all mutants. The R199A mutation abolished electron transfer between hydroquinone FprA and NADP+, while this reaction progressed (via an FADH2-NADP+ charge-transfer intermediate) for R200A FprA, albeit more slowly (klim=58.1 s−1 compared with >300 s−1) than in WT. All mutations caused positive shifts in FAD potential (∼40–65 mV). Binding of an NADPH analogue (tetrahydro-NADP) induced negative shifts in potential (∼30–40 mV) only for variants with the R200A mutation, indicating distinctive effects of Arg199/Arg200 on coenzyme binding mode and FAD potential. Collectively, these data reveal important roles for the phylogenetically conserved arginines in controlling FprA FAD environment, thermodynamics, coenzyme selectivity and reactivity.

Structural and thermodynamic insights into the binding mode of five novel inhibitors of lumazine synthase from Mycobacterium tuberculosis

FEBS Journal ◽  
2006 ◽  
Vol 273 (20) ◽  
pp. 4790-4804 ◽  
Author(s):  
Ekaterina Morgunova ◽  
Boris Illarionov ◽  
Thota Sambaiah ◽  
Ilka Haase ◽  
Adelbert Bacher ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Binding Mode ◽  
Lumazine Synthase

scholarly journals Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B12

2020 ◽  
Vol 117 (48) ◽  
pp. 30412-30422
Author(s):  
Romila Mascarenhas ◽  
Markus Ruetz ◽  
Liam McDevitt ◽  
Markos Koutmos ◽  
Ruma Banerjee
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Active Sites ◽  
Solvent Accessibility ◽  
Binding Mode ◽  
Coenzyme B12 ◽  
Coordination Geometry ◽  
Loop Dynamics ◽  
N Terminus ◽  
Bond Homolysis ◽  
Side Pocket

Cobalamin is a complex organometallic cofactor that is processed and targeted via a network of chaperones to its dependent enzymes. AdoCbl (5′-deoxyadenosylcobalamin) is synthesized from cob(II)alamin in a reductive adenosylation reaction catalyzed by adenosyltransferase (ATR), which also serves as an escort, delivering AdoCbl to methylmalonyl-CoA mutase (MCM). The mechanism by which ATR signals that its cofactor cargo is ready (AdoCbl) or not [cob(II)alamin] for transfer to MCM, is not known. In this study, we have obtained crystallographic snapshots that reveal ligand-induced ordering of the N terminus ofMycobacterium tuberculosisATR, which organizes a dynamic cobalamin binding site and exerts exquisite control over coordination geometry, reactivity, and solvent accessibility. Cob(II)alamin binds with its dimethylbenzimidazole tail splayed into a side pocket and its corrin ring buried. The cosubstrate, ATP, enforces a four-coordinate cob(II)alamin geometry, facilitating the unfavorable reduction to cob(I)alamin. The binding mode for AdoCbl is notably different from that of cob(II)alamin, with the dimethylbenzimidazole tail tucked under the corrin ring, displacing the N terminus of ATR, which is disordered. In this solvent-exposed conformation, AdoCbl undergoes facile transfer to MCM. The importance of the tail in cofactor handover from ATR to MCM is revealed by the failure of 5′-deoxyadenosylcobinamide, lacking the tail, to transfer. In the absence of MCM, ATR induces a sacrificial cobalt–carbon bond homolysis reaction in an unusual reversal of the heterolytic chemistry that was deployed to make the same bond. The data support an important role for the dimethylbenzimidazole tail in moving the cobalamin cofactor between active sites.

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