Structure elucidation of the elusive Enzyme I monomer reveals the molecular mechanisms linking oligomerization and enzymatic activity.


Journal

Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
Titre abrégé: Proc Natl Acad Sci U S A
Pays: United States
ID NLM: 7505876

Informations de publication

Date de publication:
18 05 2021
Historique:
entrez: 12 5 2021
pubmed: 13 5 2021
medline: 15 12 2021
Statut: ppublish

Résumé

Enzyme I (EI) is a phosphotransferase enzyme responsible for converting phosphoenolpyruvate (PEP) into pyruvate. This reaction initiates a five-step phosphorylation cascade in the bacterial phosphotransferase (PTS) transduction pathway. Under physiological conditions, EI exists in an equilibrium between a functional dimer and an inactive monomer. The monomer-dimer equilibrium is a crucial factor regulating EI activity and the phosphorylation state of the overall PTS. Experimental studies of EI's monomeric state have yet been hampered by the dimer's high thermodynamic stability, which prevents its characterization by standard structural techniques. In this study, we modified the dimerization domain of EI (EIC) by mutating three amino acids involved in the formation of intersubunit salt bridges. The engineered variant forms an active dimer in solution that can bind and hydrolyze PEP. Using hydrostatic pressure as an additional perturbation, we were then able to study the complete dissociation of the variant from 1 bar to 2.5 kbar in the absence and the presence of EI natural ligands. Backbone residual dipolar couplings collected under high-pressure conditions allowed us to determine the conformational ensemble of the isolated EIC monomeric state in solution. Our calculations reveal that three catalytic loops near the dimerization interface become unstructured upon monomerization, preventing the monomeric enzyme from binding its natural substrate. This study provides an atomic-level characterization of EI's monomeric state and highlights the role of the catalytic loops as allosteric connectors controlling both the activity and oligomerization of the enzyme.

Identifiants

pubmed: 33975952
pii: 2100298118
doi: 10.1073/pnas.2100298118
pmc: PMC8157928
pii:
doi:

Substances chimiques

Phosphoenolpyruvate Sugar Phosphotransferase System EC 2.7.1.-
Phosphotransferases (Nitrogenous Group Acceptor) EC 2.7.3.-
phosphoenolpyruvate-protein phosphotransferase EC 2.7.3.9

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : NIGMS NIH HHS
ID : R35 GM133488
Pays : United States

Déclaration de conflit d'intérêts

The authors declare no competing interest.

Références

J Am Chem Soc. 2010 Sep 22;132(37):13026-45
pubmed: 20731394
Methods. 2018 Sep 15;148:67-80
pubmed: 29964175
Trends Biochem Sci. 2013 Oct;38(10):515-30
pubmed: 24055245
Mol Microbiol. 2002 Sep;45(5):1389-406
pubmed: 12207705
J Biomol NMR. 2010 Oct;48(2):65-70
pubmed: 20694505
J Am Chem Soc. 2013 Oct 2;135(39):14610-8
pubmed: 23987660
J Mol Biol. 2005 Feb 18;346(2):521-32
pubmed: 15670601
Chem Rev. 2016 Jun 8;116(11):6305-22
pubmed: 26739383
J Magn Reson. 2003 Jan;160(1):65-73
pubmed: 12565051
J Comput Chem. 2005 Dec;26(16):1668-88
pubmed: 16200636
Mol Microbiol. 2000 Sep;37(6):1444-55
pubmed: 10998175
J Mol Biol. 2020 Jul 24;432(16):4481-4498
pubmed: 32504625
Res Microbiol. 1996 Jul-Sep;147(6-7):471-9
pubmed: 9084757
Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):11565-70
pubmed: 26305976
Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16218-23
pubmed: 17053069
Nat Commun. 2019 Mar 6;10(1):1068
pubmed: 30842409
Prog Nucl Magn Reson Spectrosc. 2013 May;71:35-58
pubmed: 23611314
Biophys J. 2010 Apr 21;98(8):1626-31
pubmed: 20409483
J Biol Chem. 2006 Jun 30;281(26):17579-87
pubmed: 16547354
Microb Cell Fact. 2005 May 16;4(1):14
pubmed: 15904518
Can J Biochem Cell Biol. 1983 Jan;61(1):29-37
pubmed: 6406017
Biotechnol Adv. 2019 Mar - Apr;37(2):284-305
pubmed: 30576718
NPJ Syst Biol Appl. 2017 Jan 05;3:16035
pubmed: 28725483
J Biol Chem. 2006 Jun 30;281(26):17570-8
pubmed: 16547355
J Biol Chem. 2012 Aug 3;287(32):26989-98
pubmed: 22722931
Nat Commun. 2017 Jan 27;8:14316
pubmed: 28128209
Biomol NMR Assign. 2019 Oct;13(2):287-293
pubmed: 31025174
Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):8190-5
pubmed: 10393970
J R Soc Interface. 2018 Oct 3;15(147):
pubmed: 30282759
Nat Commun. 2019 Jul 26;10(1):3354
pubmed: 31350417
Nat Chem Biol. 2011 Oct 16;7(12):894-901
pubmed: 22002719
Microbiol Mol Biol Rev. 2014 Jun;78(2):231-56
pubmed: 24847021
J Biol Chem. 2008 Jul 4;283(27):18980-9
pubmed: 18445588
J Biomol NMR. 2012 Jul;53(3):209-21
pubmed: 22689066
Protein Expr Purif. 2020 Mar;167:105540
pubmed: 31740367
Biochemistry. 2011 Feb 22;50(7):1184-93
pubmed: 21250658
Biophys J. 2018 Nov 20;115(10):1895-1905
pubmed: 30352661
J Magn Reson. 2017 Apr;277:179-185
pubmed: 28363306
J Mol Biol. 2009 Dec 18;394(5):834-42
pubmed: 19837081
J Struct Biol X. 2020 Jul 21;4:100034
pubmed: 32743545
Biochemistry. 1989 Nov 14;28(23):8972-9
pubmed: 2690953
Nat Biotechnol. 1996 May;14(5):620-3
pubmed: 9630954
Curr Opin Biotechnol. 2018 Oct;53:254-263
pubmed: 30301537
ACS Chem Biol. 2013;8(6):1232-40
pubmed: 23506042
Proc Natl Acad Sci U S A. 2012 May 1;109(18):6945-50
pubmed: 22496593
Microbiology (Reading). 2003 Sep;149(Pt 9):2645-2652
pubmed: 12949188
Nat Commun. 2015 Jan 12;6:5960
pubmed: 25581904
J Am Chem Soc. 2011 Apr 20;133(15):6020-7
pubmed: 21446709
Mol Microbiol. 2001 May;40(3):555-71
pubmed: 11359563
Methods Enzymol. 2019;614:293-320
pubmed: 30611428
J Mol Biol. 2016 Jul 3;428(13):2780-92
pubmed: 27170547
Microbiol Rev. 1993 Sep;57(3):543-94
pubmed: 8246840
J Biol Chem. 2018 Feb 16;293(7):2631-2639
pubmed: 29317499

Auteurs

Trang T Nguyen (TT)

Department of Chemistry, Iowa State University, Ames, IA 50011.

Rodolfo Ghirlando (R)

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892.

Julien Roche (J)

Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 jroche@iastate.edu venditti@iastate.edu.

Vincenzo Venditti (V)

Department of Chemistry, Iowa State University, Ames, IA 50011; jroche@iastate.edu venditti@iastate.edu.
Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011.

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Classifications MeSH