Tags

Type your tag names separated by a space and hit enter

Structure of Salmonella typhimurium OMP synthase in a complete substrate complex.
Biochemistry. 2012 Jun 05; 51(22):4397-405.B

Abstract

Dimeric Salmonella typhimurium orotate phosphoribosyltransferase (OMP synthase, EC 2.4.2.10), a key enzyme in de novo pyrimidine nucleotide synthesis, has been cocrystallized in a complete substrate E·MgPRPP·orotate complex and the structure determined to 2.2 Å resolution. This structure resembles that of Saccharomyces cerevisiae OMP synthase in showing a dramatic and asymmetric reorganization around the active site-bound ligands but shares the same basic topology previously observed in complexes of OMP synthase from S. typhimurium and Escherichia coli. The catalytic loop (residues 99-109) contributed by subunit A is reorganized to close the active site situated in subunit B and to sequester it from solvent. Furthermore, the overall structure of subunit B is more compact, because of movements of the amino-terminal hood and elements of the core domain. The catalytic loop of subunit B remains open and disordered, and subunit A retains the more relaxed conformation observed in loop-open S. typhimurium OMP synthase structures. A non-proline cis-peptide formed between Ala71 and Tyr72 is seen in both subunits. The loop-closed catalytic site of subunit B reveals that both the loop and the hood interact directly with the bound pyrophosphate group of PRPP. In contrast to dimagnesium hypoxanthine-guanine phosphoribosyltransferases, OMP synthase contains a single catalytic Mg(2+) in the closed active site. The remaining pyrophosphate charges of PRPP are neutralized by interactions with Arg99A, Lys100B, Lys103A, and His105A. The new structure confirms the importance of loop movement in catalysis by OMP synthase and identifies several additional movements that must be accomplished in each catalytic cycle. A catalytic mechanism based on enzymic and substrate-assisted stabilization of the previously documented oxocarbenium transition state structure is proposed.

Links

PMC Free PDF
PMC Free Full Text

Authors+Show Affiliations

Grubmeyer C
Department of Biochemistry and Fels Research Institute, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, United States. ctg@temple.edu
Hansen MR
No affiliation info available
Fedorov AA
No affiliation info available
Almo SC
No affiliation info available

MeSH

Catalytic DomainCrystallography, X-RayMagnesiumModels, MolecularOrotate PhosphoribosyltransferaseOrotic AcidPhosphoribosyl PyrophosphateProtein BindingProtein ConformationProtein MultimerizationSalmonella typhimurium

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural

Language

eng

PubMed ID

22531064

Citation

Grubmeyer, Charles, et al. "Structure of Salmonella Typhimurium OMP Synthase in a Complete Substrate Complex." Biochemistry, vol. 51, no. 22, 2012, pp. 4397-405.
Grubmeyer C, Hansen MR, Fedorov AA, et al. Structure of Salmonella typhimurium OMP synthase in a complete substrate complex. Biochemistry. 2012;51(22):4397-405.
Grubmeyer, C., Hansen, M. R., Fedorov, A. A., & Almo, S. C. (2012). Structure of Salmonella typhimurium OMP synthase in a complete substrate complex. Biochemistry, 51(22), 4397-405.
Grubmeyer C, et al. Structure of Salmonella Typhimurium OMP Synthase in a Complete Substrate Complex. Biochemistry. 2012 Jun 5;51(22):4397-405. PubMed PMID: 22531064.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Structure of Salmonella typhimurium OMP synthase in a complete substrate complex. AU - Grubmeyer,Charles, AU - Hansen,Michael Riis, AU - Fedorov,Alexander A, AU - Almo,Steven C, Y1 - 2012/05/23/ PY - 2012/4/26/entrez PY - 2012/4/26/pubmed PY - 2012/12/10/medline SP - 4397 EP - 405 JF - Biochemistry JO - Biochemistry VL - 51 IS - 22 N2 - Dimeric Salmonella typhimurium orotate phosphoribosyltransferase (OMP synthase, EC 2.4.2.10), a key enzyme in de novo pyrimidine nucleotide synthesis, has been cocrystallized in a complete substrate E·MgPRPP·orotate complex and the structure determined to 2.2 Å resolution. This structure resembles that of Saccharomyces cerevisiae OMP synthase in showing a dramatic and asymmetric reorganization around the active site-bound ligands but shares the same basic topology previously observed in complexes of OMP synthase from S. typhimurium and Escherichia coli. The catalytic loop (residues 99-109) contributed by subunit A is reorganized to close the active site situated in subunit B and to sequester it from solvent. Furthermore, the overall structure of subunit B is more compact, because of movements of the amino-terminal hood and elements of the core domain. The catalytic loop of subunit B remains open and disordered, and subunit A retains the more relaxed conformation observed in loop-open S. typhimurium OMP synthase structures. A non-proline cis-peptide formed between Ala71 and Tyr72 is seen in both subunits. The loop-closed catalytic site of subunit B reveals that both the loop and the hood interact directly with the bound pyrophosphate group of PRPP. In contrast to dimagnesium hypoxanthine-guanine phosphoribosyltransferases, OMP synthase contains a single catalytic Mg(2+) in the closed active site. The remaining pyrophosphate charges of PRPP are neutralized by interactions with Arg99A, Lys100B, Lys103A, and His105A. The new structure confirms the importance of loop movement in catalysis by OMP synthase and identifies several additional movements that must be accomplished in each catalytic cycle. A catalytic mechanism based on enzymic and substrate-assisted stabilization of the previously documented oxocarbenium transition state structure is proposed. SN - 1520-4995 UR - https://www.unboundmedicine.com/medline/citation/22531064/Structure_of_Salmonella_typhimurium_OMP_synthase_in_a_complete_substrate_complex_ L2 - https://doi.org/10.1021/bi300083p DB - PRIME DP - Unbound Medicine ER -