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- EMDB-45727: DosP R97A with c-di-GMP -

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Basic information

Entry
Database: EMDB / ID: EMD-45727
TitleDosP R97A with c-di-GMP
Map data
Sample
  • Complex: Dimer of DosP
    • Protein or peptide: Oxygen sensor protein DosP
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 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)
  • Ligand: MAGNESIUM ION
KeywordsHeme / DosP / Phosphodiesterase / c-di-GMP / OXYGEN BINDING
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase / regulation of single-species biofilm formation / cyclic-guanylate-specific phosphodiesterase activity / response to oxygen levels / oxygen sensor activity / heme binding / magnesium ion binding / protein homodimerization activity / plasma membrane
Similarity search - Function
Diguanylate cyclase/phosphodiesterase / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. ...Diguanylate cyclase/phosphodiesterase / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Oxygen sensor protein DosP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKumar P / Kober DL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00 GM141261 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129547 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structures of the multi-domain oxygen sensor DosP: remote control of a c-di-GMP phosphodiesterase by a regulatory PAS domain.
Authors: Wenbi Wu / Pankaj Kumar / Chad A Brautigam / Shih-Chia Tso / Hamid R Baniasadi / Daniel L Kober / Marie-Alda Gilles-Gonzalez /
Abstract: 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. ...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.
History
DepositionJul 11, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45727.png

Downloads & links

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Map

FileDownload / File: emd_45727.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 384 pix.
= 377.856 Å		0.98 Å/pix.
x 384 pix.
= 377.856 Å		0.98 Å/pix.
x 384 pix.
= 377.856 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.984 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.009348039 - 1.8145179
Average (Standard dev.)0.0004845065 (±0.012415552)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 377.856 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Dimer of DosP

EntireName: Dimer of DosP
Components
  • Complex: Dimer of DosP
    • Protein or peptide: Oxygen sensor protein DosP
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 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)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Dimer of DosP

SupramoleculeName: Dimer of DosP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Oxygen sensor protein DosP

MacromoleculeName: Oxygen sensor protein DosP / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cyclic-guanylate-specific phosphodiesterase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 89.003695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GIFFPALEQN MMGAVLINEN DEVMFFNPAA EKLWGYKREE VIGNNIDMLI PRDLRPAHPE YIRHNREGGK ARVEGMSAEL QLEKKDGSK IWTRFALSKV SAEGKVYYLA LVRDASVEMA QKEQTRQLII AVDHLDRPVI VLDPERHIVQ CNRAFTEMFG Y CISEASGM ...String:
GIFFPALEQN MMGAVLINEN DEVMFFNPAA EKLWGYKREE VIGNNIDMLI PRDLRPAHPE YIRHNREGGK ARVEGMSAEL QLEKKDGSK IWTRFALSKV SAEGKVYYLA LVRDASVEMA QKEQTRQLII AVDHLDRPVI VLDPERHIVQ CNRAFTEMFG Y CISEASGM QPDTLLNTPE FPADNRIRLQ QLLWKTARDQ DEFLLLTRTG EKIWIKASIS PVYDVLAHLQ NLVMTFSDIT EE RQIRQLE GNILAAMCSS PPFHEMGEII CRNIESVLNE SHVSLFALRN GMPIHWASSS HGAEIQNAQS WSATIRQRDG APA GILQIK TSSGAETSAF IERVADISQH MAALALEQEK SRQHIEQLIQ FDPMTGLPNR NNLHNYLDDL VDKAVSPVVY LIGV DHIQD VIDSLGYAWA DQALLEVVNR FREKLKPDQY LCRIEGTQFV LVSLENDVSN ITQIADELRN VVSKPIMIDD KPFPL TLSI GISYDLGKNR DYLLSTAHNA MDYIRKNGGN GWQFFSPAMN EMVKERLVLG AALKEAISNN QLKLVYQPQI FAETGE LYG IEALARWHDP LHGHVPPSRF IPLAEEIGEI ENIGRWVIAE ACRQLAEWRS QNIHIPALSV NLSALHFRSN QLPNQVS DA MHAWGIDGHQ LTVEITESMM MEHDTEIFKR IQILRDMGVG LSVDDFGTGF SGLSRLVSLP VTEIKIDKSF VDRCLTEK R ILALLEAITS IGQSLNLTVV AEGVETKEQF EMLRKIHCRV IQGYFFSRPL PAEEIPGWMS SVLPLK

UniProtKB: Oxygen sensor protein DosP

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydr...

MacromoleculeName: 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)
type: ligand / ID: 3 / Number of copies: 2 / Formula: C2E
Molecular weightTheoretical: 690.411 Da
Chemical component information

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)

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186761
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)

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