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- PDB-2nzu: Structural mechanism for the fine-tuning of CcpA function by the ... -

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Basic information

Entry
Database: PDB / ID: 2nzu
TitleStructural mechanism for the fine-tuning of CcpA function by the small molecule effectors G6P and FBP
Components
  • Catabolite control protein
  • Phosphocarrier protein HPr
KeywordsTRANSCRIPTION / CcpA / CCR / HPr-Ser46-P / glucose-6-phosphate / adjunct corepressor / LacI-GalR
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Catabolite control protein A / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site ...Catabolite control protein A / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-glucopyranose / Phosphocarrier protein HPr / Catabolite control protein A
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSchumacher, M.A. / Hillen, W. / Brennan, R.G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Mechanism for the Fine-tuning of CcpA Function by The Small Molecule Effectors Glucose 6-Phosphate and Fructose 1,6-Bisphosphate.
Authors: Schumacher, M.A. / Seidel, G. / Hillen, W. / Brennan, R.G.
History
DepositionNov 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Catabolite control protein
L: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,32412
Polymers40,1992
Non-polymers1,12510
Water1,22568
1
G: Catabolite control protein
L: Phosphocarrier protein HPr
hetero molecules

G: Catabolite control protein
L: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,64824
Polymers80,3994
Non-polymers2,24920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9630 Å2
ΔGint-242 kcal/mol
Surface area28570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.630, 68.630, 230.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsCcpA is dimer and each dimer binds one corepressor protein, HPr-Ser46-P. Each CcpA subunit also binds one adjunct small molecule corepressor, G6P

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Components

#1: Protein Catabolite control protein


Mass: 30992.119 Da / Num. of mol.: 1 / Fragment: residues 53-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: ccpA / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46828
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9207.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: ptsH / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O69250
#3: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.03
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 23, 2004 / Details: mirrors
RadiationMonochromator: double crystal, si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.5→45.6 Å / Num. all: 19684 / Num. obs: 19700 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.05 / Net I/σ(I): 15.2
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1900 / Rsym value: 0.3 / % possible all: 94

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1RZR

1rzr


Resolution: 2.5→58.95 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3031709.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 955 4.9 %RANDOM
Rwork0.228 ---
obs0.228 19684 98.5 %-
all-19700 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.4573 Å2 / ksol: 0.356758 e/Å3
Displacement parametersBiso mean: 66.3 Å2
Baniso -1Baniso -2Baniso -3
1-14.18 Å20 Å20 Å2
2--14.18 Å20 Å2
3----28.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→58.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 61 68 2902
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 154 4.8 %
Rwork0.321 3080 -
obs-1900 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-NEWSEP.paramprotein-NEWSEP.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4BG6_par.txtBG6_top.txt

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