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- PDB-7olh: Bacillus subtilis Complex structure 1 of diadenylate cyclase CdaA... -

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Basic information

Entry
Database: PDB / ID: 7olh
TitleBacillus subtilis Complex structure 1 of diadenylate cyclase CdaA cytoplasmic domain (CdaACD) and the phosphoglucomutase GlmM short variant (GlmMF369)
Components
  • Cyclic di-AMP synthase CdaA
  • Phosphoglucosamine mutase
KeywordsPROTEIN BINDING / Phosphoglucosamine Mutase / glucosamine-6-phosphate / glucosamine-1-phosphate / c-di-AMP / diadenylate cyclase / GlmM / CdaA / DacA / protein protein complex / isomerase / heterodimer
Function / homology
Function and homology information


phosphoglucosamine mutase / phosphoglucosamine mutase activity / phosphomannomutase activity / diadenylate cyclase / diadenylate cyclase activity / UDP-N-acetylglucosamine biosynthetic process / cAMP biosynthetic process / adenylate cyclase activity / peptidoglycan biosynthetic process / carbohydrate metabolic process ...phosphoglucosamine mutase / phosphoglucosamine mutase activity / phosphomannomutase activity / diadenylate cyclase / diadenylate cyclase activity / UDP-N-acetylglucosamine biosynthetic process / cAMP biosynthetic process / adenylate cyclase activity / peptidoglycan biosynthetic process / carbohydrate metabolic process / magnesium ion binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
Phosphoglucosamine mutase, bacterial type / : / Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / Alpha-D-phosphohexomutase, C-terminal / : / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily ...Phosphoglucosamine mutase, bacterial type / : / Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / Alpha-D-phosphohexomutase, C-terminal / : / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile. / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglucosamine mutase / Cyclic di-AMP synthase CdaA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsPathania, M. / Grundling, A.G. / Freemont, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)P63775 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis for the inhibition of the Bacillus subtilis c-di-AMP cyclase CdaA by the phosphoglucomutase GlmM.
Authors: Pathania, M. / Tosi, T. / Millership, C. / Hoshiga, F. / Morgan, R.M.L. / Freemont, P.S. / Grundling, A.
History
DepositionMay 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglucosamine mutase
B: Phosphoglucosamine mutase
C: Phosphoglucosamine mutase
D: Phosphoglucosamine mutase
E: Phosphoglucosamine mutase
F: Phosphoglucosamine mutase
G: Cyclic di-AMP synthase CdaA
H: Cyclic di-AMP synthase CdaA
I: Cyclic di-AMP synthase CdaA
J: Cyclic di-AMP synthase CdaA
K: Cyclic di-AMP synthase CdaA
L: Cyclic di-AMP synthase CdaA


Theoretical massNumber of molelcules
Total (without water)412,54712
Polymers412,54712
Non-polymers00
Water00
1
A: Phosphoglucosamine mutase
B: Phosphoglucosamine mutase
I: Cyclic di-AMP synthase CdaA
J: Cyclic di-AMP synthase CdaA


Theoretical massNumber of molelcules
Total (without water)137,5164
Polymers137,5164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Phosphoglucosamine mutase
D: Phosphoglucosamine mutase
G: Cyclic di-AMP synthase CdaA
H: Cyclic di-AMP synthase CdaA


Theoretical massNumber of molelcules
Total (without water)137,5164
Polymers137,5164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Phosphoglucosamine mutase
F: Phosphoglucosamine mutase
K: Cyclic di-AMP synthase CdaA
L: Cyclic di-AMP synthase CdaA


Theoretical massNumber of molelcules
Total (without water)137,5164
Polymers137,5164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.205, 227.561, 151.604
Angle α, β, γ (deg.)90.000, 99.660, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 82 or resid 84 through 368))
21(chain B and (resid 3 through 82 or resid 84 through 368))
31(chain C and (resid 3 through 82 or resid 84 through 368))
41(chain D and (resid 3 through 82 or resid 84 through 368))
51(chain E and (resid 3 through 82 or resid 84 through 368))
61(chain F and (resid 3 through 82 or resid 84 through 368))
12(chain G and (resid 107 through 194 or resid 198 through 252))
22(chain H and resid 107 through 252)
32(chain I and (resid 107 through 194 or resid 198 through 252))
42(chain J and (resid 107 through 194 or resid 198 through 252))
52(chain K and (resid 107 through 194 or resid 198 through 252))
62(chain L and resid 107 through 252)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSVALVAL(chain A and (resid 3 through 82 or resid 84 through 368))AA3 - 823 - 82
121TYRTYRLYSLYS(chain A and (resid 3 through 82 or resid 84 through 368))AA84 - 36884 - 368
211LYSLYSVALVAL(chain B and (resid 3 through 82 or resid 84 through 368))BB3 - 823 - 82
221TYRTYRLYSLYS(chain B and (resid 3 through 82 or resid 84 through 368))BB84 - 36884 - 368
311LYSLYSVALVAL(chain C and (resid 3 through 82 or resid 84 through 368))CC3 - 823 - 82
321TYRTYRLYSLYS(chain C and (resid 3 through 82 or resid 84 through 368))CC84 - 36884 - 368
411LYSLYSVALVAL(chain D and (resid 3 through 82 or resid 84 through 368))DD3 - 823 - 82
421TYRTYRLYSLYS(chain D and (resid 3 through 82 or resid 84 through 368))DD84 - 36884 - 368
511LYSLYSVALVAL(chain E and (resid 3 through 82 or resid 84 through 368))EE3 - 823 - 82
521TYRTYRLYSLYS(chain E and (resid 3 through 82 or resid 84 through 368))EE84 - 36884 - 368
611LYSLYSVALVAL(chain F and (resid 3 through 82 or resid 84 through 368))FF3 - 823 - 82
621TYRTYRLYSLYS(chain F and (resid 3 through 82 or resid 84 through 368))FF84 - 36884 - 368
112GLUGLUPROPRO(chain G and (resid 107 through 194 or resid 198 through 252))GG107 - 1941 - 88
122LYSLYSGLUGLU(chain G and (resid 107 through 194 or resid 198 through 252))GG198 - 25292 - 146
212GLUGLUGLUGLU(chain H and resid 107 through 252)HH107 - 2521 - 146
312GLUGLUPROPRO(chain I and (resid 107 through 194 or resid 198 through 252))II107 - 1941 - 88
322LYSLYSGLUGLU(chain I and (resid 107 through 194 or resid 198 through 252))II198 - 25292 - 146
412GLUGLUPROPRO(chain J and (resid 107 through 194 or resid 198 through 252))JJ107 - 1941 - 88
422LYSLYSGLUGLU(chain J and (resid 107 through 194 or resid 198 through 252))JJ198 - 25292 - 146
512GLUGLUPROPRO(chain K and (resid 107 through 194 or resid 198 through 252))KK107 - 1941 - 88
522LYSLYSGLUGLU(chain K and (resid 107 through 194 or resid 198 through 252))KK198 - 25292 - 146
612GLUGLUGLUGLU(chain L and resid 107 through 252)LL107 - 2521 - 146

NCS ensembles :
ID
1
2

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Components

#1: Protein
Phosphoglucosamine mutase


Mass: 50314.867 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: glmM, ybbT, BSU01770 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O34824, phosphoglucosamine mutase
#2: Protein
Cyclic di-AMP synthase CdaA / c-di-AMP synthase / Diadenylate cyclase / DAC


Mass: 18442.963 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: cdaA, ybbP, BSU01750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q45589, diadenylate cyclase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.12 M alcohols, 0.1 M buffer system (Imidazole; MES, pH 6.5) and 30% GOL_P4K (60% glycerol, PEG 4K)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.65→61.323 Å / Num. obs: 45925 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rpim(I) all: 0.019 / Net I/σ(I): 5.5
Reflection shellResolution: 3.65→3.78 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4441 / CC1/2: 0.53 / Rpim(I) all: 0.153

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dimers of B. subtilis GlmMF369 and CdaACD

Resolution: 3.65→61.32 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 2175 4.75 %
Rwork0.2418 43642 -
obs0.2428 45817 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.79 Å2 / Biso mean: 108.7223 Å2 / Biso min: 52.5 Å2
Refinement stepCycle: final / Resolution: 3.65→61.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23139 0 0 0 23139
Num. residues----3076
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10347X-RAY DIFFRACTION14.175TORSIONAL
12B10347X-RAY DIFFRACTION14.175TORSIONAL
13C10347X-RAY DIFFRACTION14.175TORSIONAL
14D10347X-RAY DIFFRACTION14.175TORSIONAL
15E10347X-RAY DIFFRACTION14.175TORSIONAL
16F10347X-RAY DIFFRACTION14.175TORSIONAL
21G4107X-RAY DIFFRACTION14.175TORSIONAL
22H4107X-RAY DIFFRACTION14.175TORSIONAL
23I4107X-RAY DIFFRACTION14.175TORSIONAL
24J4107X-RAY DIFFRACTION14.175TORSIONAL
25K4107X-RAY DIFFRACTION14.175TORSIONAL
26L4107X-RAY DIFFRACTION14.175TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.6501-3.72940.36121550.3521265199
3.7294-3.81620.34751260.3175273699
3.8162-3.91160.30781270.3164275999
3.9116-4.01730.34641180.2982267699
4.0173-4.13550.32071340.2853278899
4.1355-4.2690.28981410.2612268599
4.269-4.42150.25561220.2546274499
4.4215-4.59850.28841400.25612711100
4.5985-4.80770.25141310.24622761100
4.8077-5.0610.27121300.24222701100
5.061-5.37790.23361220.24142742100
5.3779-5.79290.34311230.25432764100
5.7929-6.37530.24641410.24682740100
6.3753-7.29650.24191710.242694100
7.2965-9.18790.19721440.18552763100
9.1879-61.30.21711500.1814272798

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