Crystal structure of formycin 5'-phosphate: an explanation for its tight binding to AMP nucleosidase

Giranda, Vincent L.; Berman, Helen M.; Schramm, Vern L.

doi:10.1021/bi00415a062

“…Substrate and inhibitor specificity studies revealed that formycin A 5 -phosphate binds >10 3 times tighter to AMP nucleosidases than does substrate (59,60). The X-ray crystal structure of this inhibitor helped to establish the properties of the transition state (61). The inhibitor has a syn-ribosyl torsion angle, preferred in all nucleotide inhibitors of the enzyme (59).…”

Section: Amp Nucleosidasementioning

confidence: 99%

Enzymatic Transition States and Transition State Analog Design

Schramm

¹

1998

Annu. Rev. Biochem.

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All chemical transformations pass through an unstable structure called the transition state, which is poised between the chemical structures of the substrates and products. The transition states for chemical reactions are proposed to have lifetimes near 10 −13 sec, the time for a single bond vibration. No physical or spectroscopic method is available to directly observe the structure of the transition state for enzymatic reactions. Yet transition state structure is central to understanding catalysis, because enzymes function by lowering activation energy. An accepted view of enzymatic catalysis is tight binding to the unstable transition state structure. Transition state mimics bind tightly to enzymes by capturing a fraction of the binding energy for the transition state species. The identification of numerous transition state inhibitors supports the transition state stabilization hypothesis for enzymatic catalysis. Advances in methods for measuring and interpreting kinetic isotope effects and advances in computational chemistry have provided an experimental route to understand transition state structure. Systematic analysis of intrinsic kinetic isotope effects provides geometric and electronic structure for enzyme-bound transition states. This information has been used to compare transition states for chemical and enzymatic reactions; determine whether enzymatic activators alter transition state structure; design transition state inhibitors; and provide the basis for predicting the affinity of enzymatic inhibitors. Enzymatic transition states provide an understanding of catalysis and permit the design of transition state inhibitors. This article reviews transition state theory for enzymatic reactions. Selected examples of enzymatic transition states are compared to the respective transition state inhibitors.

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“…It is also an important probe of nucleoside transport (17)(18)(19)(20)(21). The tight binding of formycin 5 -phosphate to adenoside monophosphate (AMP) deaminase has been reported (22). Compound (12) has been used to elucidate ribosome-transfer RNA (tRNA) interactions and it has been reported that the stacking of tRNA PheCCF , where the tail is phenylalanine-cytosine-cytosine-formycin, is weaker than that of tRNA PheCCA (23,24).…”

Section: Pyrazomycinmentioning

confidence: 99%

Nucleosides and Nucleotides

Suhadolnik¹,

Reichenbach²

2000

Kirk-Othmer Encyclopedia of Chemical Technology

1

0

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The naturally occurring nucleoside and nucleotide antibiotics exist as either the C ‐ or N ‐glycosides. They include ezomycin A 1 (C 26 H 38 N 8 O 15 S), ezomycin B 1 (C 26 H 39 N 7 O 17 S), ezomycin C 1 (C 26 H 37 N 7 O 16 S), ezomycin A 2 (C 19 H 26 N 6 O 12 ), ezomycin B 2 (C 19 H 25 N 5 O 13 ), ezomycin C 2 (C 19 H 25 N 5 O 13 ), showdomycin (C 9 H 11 NO 6 ), isoshowdomycin (C 9 H 11 NO 6 ), maleimycin (C 7 H 7 NO 3 ), oxazinomycin (C 9 H 11 NO 7 ), pyrazomycin (pyrazofurin) (C 9 H 13 N 3 O 6 ), formycin (C 10 H 13 N 5 O 4 ), formycin B (C 10 H 12 N 4 O 5 ), oxoformycin B (C 10 H 12 N 4 O 6 ). These antibiotics contain a variety of purine and pyrimidine rings. The naturally occurring nucleoside/nucleotide antibiotics, which have been isolated from bacteria, fungi, blue‐green algae, and marine sponges, have proven to be useful biochemical probes in eucaryotic, procaryotic, viral, fungal, and plant systems. The purine nucleosides inhibit protein synthesis, RNA and DNA synthesis, and methyltransferases; they have antimycoplasmal, antiviral, hypotensive, antifungal, antimycobacterial, and antitumor activities and induce sporulation. The pyrimidine nucleosides inhibit protein synthesis, virus replication, RNA and DNA synthesis, and cAMP phosphodiesterase. The imidazole nucleosides inhibit nucleic acid synthesis. The diazepin nucleosides inhibit adenosine deaminase (ADA). The indole nucleosides inhibit bacteria, yeast, fungi, and viruses. The N ‐nucleotide antibiotics include agrocin 84 (C 21 H 34 N 6 O 16 P 2 ), thuringiensin (C 22 H 30 N 5 O 19 P), phosmidosine (C 16 H 24 N 7 O 8 P), fosfadecin (C 13 H 19 N 5 O 10 P 2 ), and fosfocytocin (C 12 H 20 N 4 O 13 P 2 ). Thuringiensin, produced by B. thuringiensis , is a β‐exotoxin that exerts its toxic action on insects and mammals through the inhibition of RNA polymerases. Phosmidosine inhibits pore formation of Botrytis cinerea and Aspergillus niger . Fosfadecin and fosfocytocin inhibit gram‐positive and gram‐negative bacteria.

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“…Recently, the active site of RTA was characterized from the X-ray structure of the binding of formycin 5'-monophosphate (FMP) and adenylyl-3',5'-guanosine (ApG) [24], two nucleotide ligands thought to mimic certain structural interactions of the rRNA substrate. The ligand FMP has been shown by Schramm and co-workers [25,26] to be a strong competitive inhibitor of the mechanistically related enzyme, AMP nucleosidase, to which it binds 1200-to 2600-fold more tightly (depending on the source of the enzyme) than the normal substrate, AMR The tight binding of FMP (attributed to a syn conformational binding mode [27]) and its structural similarity to AMP suggest that FMP may be a transition-state analog for the N-glycosidase reaction. For ricin A-chain, however, it has been shown that FMP is not an inhibitor, nor a strong binding ligand [24].…”

Section: Introductionmentioning

confidence: 99%

“…1), and from amino substitution at the ribose 2'-position. Because of the lack of specific interactions of the FMP phosphate group with protein atoms observed in the X-ray structure, combined with the ambiguity in treating the ionization state of FMP within the RTA active site, several different simulation models of the enzyme-ligand complex were considered, corresponding to full and partial ionization of the phosphate group, as well as a zwitterion in which N-3 of the formycin ring was protonated, as suggested by the known X-ray crystal structure of unbound FMP [27]. Structural binding interactions for each of the simulation models together with the crystal structure were characterized at the level of electrostatic and van der Waals interactions for key individual residues in the RTA active site.…”

Section: Introductionmentioning

confidence: 99%

Simulation analysis of formycin 5?-monophosphate analog substrates in the ricin A-chain active site

Olson

¹

,

Scovill

²

,

Hack

³

1995

J Computer-Aided Mol Des

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Ricin is an RNA N-glycosidase that hydrolyzes a single adenine base from a conserved loop of 28S ribosomal RNA, thus inactivating protein synthesis. Molecular-dynamics simulation methods are used to analyze the structural interactions and thermodynamics that govern the binding of formycin 5'-monophosphate (FMP) and several of its analogs to the active site of ricin A-chain. Simulations are carried out initiated from the X-ray crystal structure of the ricin-FMP complex with the ligand modeled as a dianion, monoanion and zwitterion. Relative changes in binding free energies are estimated for FMP analogs constructed from amino substitutions at the 2- and 2'-positions, and from hydroxyl substitution at the 2'-position.

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Crystal structure of formycin 5'-phosphate: an explanation for its tight binding to AMP nucleosidase

Cited by 25 publications

References 27 publications

Enzymatic Transition States and Transition State Analog Design

Enzymatic Transition States and Transition State Analog Design

Nucleosides and Nucleotides

Simulation analysis of formycin 5?-monophosphate analog substrates in the ricin A-chain active site

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