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TitleStructures of the multi-domain oxygen sensor DosP: remote control of a c-di-GMP phosphodiesterase by a regulatory PAS domain.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 9653, Year 2024
Publish dateNov 7, 2024
AuthorsWenbi Wu / Pankaj Kumar / Chad A Brautigam / Shih-Chia Tso / Hamid R Baniasadi / Daniel L Kober / Marie-Alda Gilles-Gonzalez /
PubMed AbstractThe heme-based direct oxygen sensor DosP degrades c-di-GMP, a second messenger nearly unique to bacteria. In stationary phase Escherichia coli, DosP is the most abundant c-di-GMP phosphodiesterase. ...The heme-based direct oxygen sensor DosP degrades c-di-GMP, a second messenger nearly unique to bacteria. In stationary phase Escherichia coli, DosP is the most abundant c-di-GMP phosphodiesterase. Ligation of O to a heme-binding PAS domain (hPAS) of the protein enhances the phosphodiesterase through an allosteric mechanism that has remained elusive. We determine six structures of full-length DosP in its aerobic or anaerobic conformations, with or without c-di-GMP. DosP is an elongated dimer with the regulatory heme containing domain and phosphodiesterase separated by nearly 180 Å. In the absence of substrate, regardless of the heme status, DosP presents an equilibrium of two distinct conformations. Binding of substrate induces DosP to adopt a single, ON-state or OFF-state conformation depending on its heme status. Structural and biochemical studies of this multi-domain sensor and its mutants provide insights into signal regulation of second-messenger levels.
External linksNat Commun / PubMed:39511182 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 4.21 Å
Structure data

44524

9bgv

EMDB-44524, PDB-9bgv:
DosP R97A straight form
Method: EM (single particle) / Resolution: 3.65 Å

44646

9bkv

EMDB-44646, PDB-9bkv:
DosP R97A bent form
Method: EM (single particle) / Resolution: 3.43 Å

45485

9cdr

EMDB-45485, PDB-9cdr:
DosP Apo straight form
Method: EM (single particle) / Resolution: 3.91 Å

45489

9ce0

EMDB-45489, PDB-9ce0:
DosP Apo Bent form
Method: EM (single particle) / Resolution: 3.97 Å

EMDB-45645: C-terminal Map of the Wild type DosP with C-Di-GMP substrate
Method: EM (single particle) / Resolution: 3.11 Å

EMDB-45646: N-terminal Map of the Wild type DosP with C-Di-GMP substrate
Method: EM (single particle) / Resolution: 4.21 Å

EMDB-45665: DosP with substrate consensus map
Method: EM (single particle) / Resolution: 3.69 Å

EMDB-45669: DosP-R97A with substrate, N-terminal map
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-45670: DosP-R97A with substrate, consensus map
Method: EM (single particle) / Resolution: 3.45 Å

45727

9clo

EMDB-45727, PDB-9clo:
DosP R97A with c-di-GMP
Method: EM (single particle) / Resolution: 3.1 Å

45746

9cmf

EMDB-45746, PDB-9cmf:
Substrate bound DosP
Method: EM (single particle) / Resolution: 3.11 Å

Chemicals

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-OXY:
OXYGEN MOLECULE

ChemComp-C2E:
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)

ChemComp-MG:
Unknown entry

Source
  • E.coli (others)
  • escherichia coli (E. coli)
KeywordsOXYGEN BINDING / Heme / DosP / Phosphodiesterase / c-di-GMP

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