Crystallization of native and selenomethionyl yeast orotidine 5′-phosphate decarboxylase

Miller, Brian G.; Hassell, Anne M.; Milburn, Michael V.; Short, Steven A.

doi:10.1107/s0907444900000949

Cited by 3 publications

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“…For 6-cyano-UMP, such a distortion receives strong support from Raman spectroscopy, which indicates bond bending of about 20°(15). The crystal structure of ODCase from Plasmodium falciparum in complex with OMP (16) The binding affinity of UMP, however, is significantly weaker than that of the substrate OMP and other UMP derivatives with negatively charged substituents at C6 (17)(18)(19)(20), an obviously serious argument against such an interpretation (18, 21). The low affinity of UMP seems inconsistent with the substrate distortion mechanism because UMP has lost its carboxylate group and with it the main candidate for repulsion with Asp-70.…”

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confidence: 99%

Atomic Resolution Structure of the Orotidine 5′-Monophosphate Decarboxylase Product Complex Combined with Surface Plasmon Resonance Analysis

Fujihashi

Mito

Pai

et al. 2013

Journal of Biological Chemistry

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Background: Low binding affinity of product UMP is used to argue against substrate distortion contributing to orotidine-5Ј-monophosphate decarboxylase catalysis. Results: Atomic resolution structure and surface plasmon resonance analysis reveal strong repulsion between active site residue and UMP. Conclusion: Low UMP affinity does not disprove contribution of substrate distortion to catalysis. Significance: Substrate distortion can still be considered as a mechanistic feature of this most proficient enzyme.Orotidine 5-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of its substrate by 17 orders of magnitude. One argument brought forward against steric/electrostatic repulsion causing substrate distortion at the carboxylate substituent as part of the catalysis has been the weak binding affinity of the decarboxylated product (UMP). The crystal structure of the UMP complex of ODCase at atomic resolution (1.03 Å) shows steric competition between the product UMP and the side chain of a catalytic lysine residue. Surface plasmon resonance analysis indicates that UMP binds 5 orders of magnitude more tightly to a mutant in which the interfering side chain has been removed than to wild-type ODCase. These results explain the low affinity of UMP and counter a seemingly very strong argument against a contribution of substrate distortion to the catalytic reaction mechanism of ODCase.Orotidine 5Ј-monophosphate decarboxylase (ODCase) 3 is one of the most proficient enzymes known (1). It decarboxylates orotidine 5Ј-monophosphate (OMP) and produces uridine 5Ј-monophosphate (UMP) in the final step of the de novo pyrimidine biosynthesis pathway (Fig. 1A). It also accelerates the reaction by 17 orders of magnitude, as compared with the spontaneous reaction in water at neutral pH, without employing cofactors or metal ions (1-5).The reaction mechanism of this enzyme has been the subject of extensive investigations. More than 170 crystal structures have been determined, and numerous kinetic assays at various conditions have been performed. These experiments established that an electrostatic residue network composed of the charged side chains of two aspartate and two lysine residues, all completely conserved, plays a dominant role in catalysis (Fig. 1B) (2-5). As with all enzymes, the reaction acceleration provided by ODCase is explained in part by transition state stabilization (6). Lys-72 (the sequence numbers in this study correspond to those of the ODCase from Methanothermobacter thermautotrophicus (MtODCase)) is considered to be the key residue to stabilize the intermediate vinyl anion (6,7). However, there is still no general agreement on all the details of the reaction mechanism. In particular, the observation that ODCase also converts 6-cyano-UMP into 6-hydroxy-UMP at the same site where the decarboxylation reaction occurs (Fig. 1A) (8) complicates the scenario. The environment required to stabilize the vinyl anion does not seem suitable to support, at the same time, the intermediate of the side reaction b...

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confidence: 99%

Atomic Resolution Structure of the Orotidine 5′-Monophosphate Decarboxylase Product Complex Combined with Surface Plasmon Resonance Analysis

Fujihashi

Mito

Pai

et al. 2013

Journal of Biological Chemistry

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“…Structure In 2000 the first crystal structures of orotidine-5'-monophosphate-decarboxylase from the organism B. subtilis, E. coli, M. thermoautotrophicum and S. cervisiae were published and provided new insights into the general structure of OMPD. [11]- [14] Crystal structures of OMPDs from other organisms followed a few years later, including human OMPD. [15], [16] This new information lead to better understanding of the enzyme structure.…”

Section: Orotidine-5'-monophosphate-decarboxylase (Ompd)mentioning

confidence: 99%

“…Mainly, the phosphate gripper loop is moving towards the active site, caused by hydrogen bonding of Gln 430 to the pyrimidine part of the ligand, closing the active site and resulting in exclusion of solvent molecules. [14], [35] Additionally, movement of some α-helices closer the active site causing rearrangement of some amino acid residues involved in substrate binding as well as a minor rearrangement of the catalytic tetrad.…”

Section: Substrate Bindingmentioning

confidence: 99%

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Synthesis of rare nucleobases and artificial nucleotides for investigation of catalytic enzyme activity

Krüll¹

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Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine", Scientific Reports, 2018, 8:8880. Declaration of AuthorshipHereby, I declare that I prepared the doctoral thesis entitled "Synthesis of rare nucleobases and artificial nucleotides for investigation of catalytic enzyme activity" on my own and with no other sources and aids than quoted.Göttingen, August 2019 MATTHIAS KRULL Dedicated to my parents 3.5.9. 2',3'-O-Isopropylidene-queuine (144) .

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In order to keep subscribers up‐to‐date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly‐published material on yeasts. Each bibliography is divided into 10 sections. 1 Books, Reviews & Symposia; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (3 weeks journals ‐ search completed 21st June 2000)

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Crystallization of native and selenomethionyl yeast orotidine 5′-phosphate decarboxylase

Cited by 3 publications

References 13 publications

Atomic Resolution Structure of the Orotidine 5′-Monophosphate Decarboxylase Product Complex Combined with Surface Plasmon Resonance Analysis

Atomic Resolution Structure of the Orotidine 5′-Monophosphate Decarboxylase Product Complex Combined with Surface Plasmon Resonance Analysis

Synthesis of rare nucleobases and artificial nucleotides for investigation of catalytic enzyme activity

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