3G24

Crystal structure of the mutant D70N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

PDB DOI: https://doi.org/10.2210/pdb3G24/pdb

Classification: LYASE
Organism(s): Methanothermobacter thermautotrophicus str. Delta H
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-01-30 Released: 2009-06-23
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Chan, K.K., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.197
R-Value Work: 0.183
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.

Chan, K.K., Wood, B.M., Fedorov, A.A., Fedorov, E.V., Imker, H.J., Amyes, T.L., Richard, J.P., Almo, S.C., Gerlt, J.A.

(2009) Biochemistry 48: 5518-5531

PubMed: 19435314 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/bi900623r
Primary Citation of Related Structures:
3G18, 3G1A, 3G1D, 3G1F, 3G1H, 3G1S, 3G1V, 3G1X, 3G1Y, 3G22, 3G24, 3GDK, 3GDL, 3GDR, 3GDT

PubMed Abstract:
The reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) involves a stabilized anionic intermediate, although the structural basis for the rate acceleration (k(cat)/k(non), 7.1 x 10(16)) and proficiency [(k(cat)/K(M))/k(non), 4.8 x 10(22) M(-1)] is uncertain. That the OMPDCs from Methanothermobacter thermautotrophicus (MtOMPDC) and Saccharomyces cerevisiae (ScOMPDC) catalyze the exchange of H6 of the UMP product with solvent deuterium allows an estimate of a lower limit on the rate acceleration associated with stabilization of the intermediate and its flanking transition states (>or=10(10)). The origin of the "missing" contribution, or=10(10)), is of interest. Based on structures of liganded complexes, unfavorable electrostatic interactions between the substrate carboxylate group and a proximal Asp (Asp 70 in MtOMPDC and Asp 91 in ScOMPDC) have been proposed to contribute to the catalytic efficiency [Wu, N., Mo, Y., Gao, J., and Pai, E. F. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 2017-2022]. We investigated that hypothesis by structural and functional characterization of the D70N and D70G mutants of MtOMPDC and the D91N mutant of ScOMPDC. The substitutions for Asp 70 in MtOMPDC significantly decrease the value of k(cat) for decarboxylation of FOMP (a more reactive substrate analogue) but have little effect on the value of k(ex) for exchange of H6 of FUMP with solvent deuterium; the structures of wild-type MtOMPDC and its mutants are superimposable when complexed with 6-azaUMP. In contrast, the D91N mutant of ScOMPDC does not catalyze exchange of H6 of FUMP; the structures of wild-type ScOMPDC and its D91N mutant are not superimposable when complexed with 6-azaUMP, with differences in both the conformation of the active site loop and the orientation of the ligand vis a vis the active site residues. We propose that the differential effects of substitutions for Asp 70 of MtOMPDC on decarboxylation and exchange provide additional evidence for a carbanionic intermediate as well as the involvement of Asp 70 in substrate destabilization.

Organizational Affiliation

Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

Macromolecule Content

Total Structure Weight: 50.42 kDa
Atom Count: 3,641
Modelled Residue Count: 435
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	228	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 2 Gene Names: pyrF, MTH_129 EC: 4.1.1.23
UniProt
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26232 Go to UniProtKB: O26232
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O26232
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UP6 Query on UP6 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	6-AZA URIDINE 5'-MONOPHOSPHATE C₈ H₁₂ N₃ O₉ P LRVZOSYMNMNQFR-SHUUEZRQSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]