3PBW

Crystal structure of the mutant L123N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

Summary for 3PBW

• Entry DOI: 10.2210/pdb3pbw/pdb
• Related: 3G18 3LHW 3LTP 3LTS 3LTY 3LV5 3LV6 3NQ6 3NQ7 3NQA 3NQC 3NQD 3NQE 3NQF 3NQG 3NQM 3P5Y 3P5Z 3P60 3P61 3PBU 3PBV 3PBY 3PC0 3SIZ 3SY5
• Descriptor: Orotidine 5'-monophosphate decarboxylase, 6-AZA URIDINE 5'-MONOPHOSPHATE (3 entities in total)
• Functional Keywords: tim barrel, orotidine 5'-monophosphate decarboxylase, 6-azauridine 5'-monophosphate, lyase
• Biological source: Methanobacterium thermoautotrophicum
• Total number of polymer chains: 2
• Total formula weight: 50421.62

Authors

Fedorov, A.A.,Fedorov, E.V.,Iiams, V.,Wood, B.M.,Gerlt, J.A.,Almo, S.C. (deposition date: 2010-10-21, release date: 2011-09-21, Last modification date: 2023-09-06)

Primary citation

Iiams, V.,Desai, B.J.,Fedorov, A.A.,Fedorov, E.V.,Almo, S.C.,Gerlt, J.A.
Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.
Biochemistry, 50:8497-8507, 2011

PubMed Abstract: The reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) is accompanied by exceptional values for rate enhancement (k(cat)/k(non) = 7.1 × 10(16)) and catalytic proficiency [(k(cat)/K(M))/k(non) = 4.8 × 10(22) M(-1)]. Although a stabilized vinyl carbanion/carbene intermediate is located on the reaction coordinate, the structural strategies by which the reduction in the activation energy barrier is realized remain incompletely understood. This laboratory recently reported that "substrate destabilization" by Asp 70 in the OMPDC from Methanothermobacter thermoautotrophicus (MtOMPDC) lowers the activation energy barrier by ∼5 kcal/mol (contributing ~2.7 × 10(3) to the rate enhancement) [Chan, K. K., Wood, B. M., Fedorov, A. A., Fedorov, E. V., Imker, H. J., Amyes, T. L., Richard, J. P., Almo, S. C., and Gerlt, J. A. (2009) Biochemistry 48, 5518-5531]. We now report that substitutions of hydrophobic residues in a pocket proximal to the carboxylate group of the substrate (Ile 96, Leu 123, and Val 155) with neutral hydrophilic residues decrease the value of k(cat) by as much as 400-fold but have a minimal effect on the value of k(ex) for exchange of H6 of the FUMP product analogue with solvent deuterium; we hypothesize that this pocket destabilizes the substrate by preventing hydration of the substrate carboxylate group. We also report that substitutions of Ser 127 that is proximal to O4 of the orotate ring decrease the value of k(cat)/K(M), with the S127P substitution that eliminates hydrogen bonding interactions with O4 producing a 2.5 × 10(6)-fold reduction; this effect is consistent with delocalization of the negative charge of the carbanionic intermediate on O4 that produces an anionic carbene intermediate and thereby provides a structural strategy for stabilization of the intermediate. These observations provide additional information about the identities of the active site residues that contribute to the rate enhancement and, therefore, insights into the structural strategies for catalysis.

PubMed: 21870810
DOI: 10.1021/bi2012355

Experimental method

X-RAY DIFFRACTION (1.3 Å)