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- PDB-2mp0: Protein Phosphorylation upon a Fleeting Encounter -

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Basic information

Entry
Database: PDB / ID: 2mp0
TitleProtein Phosphorylation upon a Fleeting Encounter
Components
  • Glucose-specific phosphotransferase enzyme IIA component
  • Phosphoenolpyruvate-protein phosphotransferasePhosphoenolpyruvate—protein phosphotransferase
KeywordsTRANSFERASE / EIN EIIAGlc complex
Function / homology
Function and homology information


negative regulation of carbohydrate metabolic process / phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation ...negative regulation of carbohydrate metabolic process / phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / membrane / identical protein binding / metal ion binding / cytosol
Similarity search - Function
PtsI, HPr-binding domain / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Phosphotransferase system, enzyme I / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / PEP-utilising enzyme, N-terminal ...PtsI, HPr-binding domain / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Phosphotransferase system, enzyme I / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / PEP-utilising enzyme, N-terminal / Phosphohistidine domain / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Duplicated hybrid motif / Enzyme I; Chain A, domain 2 / Glucose Oxidase; domain 1 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Distorted Sandwich / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHITE ION / Phosphoenolpyruvate-protein phosphotransferase / PTS system glucose-specific EIIA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsXing, Q. / Yang, J. / Huang, P. / Zhang, W. / Tang, C.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Visualizing an ultra-weak protein-protein interaction in phosphorylation signaling.
Authors: Xing, Q. / Huang, P. / Yang, J. / Sun, J.Q. / Gong, Z. / Dong, X. / Guo, D.C. / Chen, S.M. / Yang, Y.H. / Wang, Y. / Yang, M.H. / Yi, M. / Ding, Y.M. / Liu, M.L. / Zhang, W.P. / Tang, C.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Visualizing an Ultra-Weak Protein-Protein Interaction in Phosphorylation Signaling
Authors: Xing, Q. / Huang, P. / Yang, J. / Sun, J. / Gong, Z. / Dong, X. / Guo, D. / Chen, S. / Yang, Y. / Wang, Y. / Yang, M. / Yi, M. / Ding, Y. / Liu, M. / Zhang, W. / Tang, C.
History
DepositionMay 8, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate-protein phosphotransferase
B: Glucose-specific phosphotransferase enzyme IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4453
Polymers46,3662
Non-polymers791
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 90structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Phosphoenolpyruvate-protein phosphotransferase / Phosphoenolpyruvate—protein phosphotransferase / Phosphotransferase system / enzyme I


Mass: 28224.121 Da / Num. of mol.: 1 / Fragment: N-terminal Domain, residues 1-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ptsI / Production host: Escherichia coli (E. coli) / Strain (production host): G1698
References: UniProt: P08839, phosphoenolpyruvate-protein phosphotransferase
#2: Protein Glucose-specific phosphotransferase enzyme IIA component / EIIA-Glc / EIII-Glc / PTS system glucose-specific EIIA component


Mass: 18141.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: crr / Production host: Escherichia coli (E. coli)
References: UniProt: P69783, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 15N] N-terminal Domain of Enzyme I-1, 0.5 mM [U-99% 15N] Enzyme II of Glucose-2, 90% H2O/10% D2O90% H2O/10% D2O
21-14 mM [U-100% 1H; U-100% 12C; U-99%1 5N] N-terminal Domain of Enzyme I-3, 1-14 mM [U-99% 15N] EIN EIIAGlc-4, 1-14 mM EIN-5, 90% H2O/10% D2O90% H2O/10% D2O
31.4-1.5 mM [U-100% 2H; U-100% 12C; U-99% 15N] N-terminal Domain of Enzyme I-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.5 mMN-terminal Domain of Enzyme I-1[U-99% 15N]1
0.5 mMEnzyme II of Glucose-2[U-99% 15N]1
mMN-terminal Domain of Enzyme I-3[U-100% 1H; U-100% 12C; U-99%1 5N]1-142
mMEIN EIIAGlc-4[U-99% 15N]1-142
mMEIN-51-142
mMN-terminal Domain of Enzyme I-6[U-100% 2H; U-100% 12C; U-99% 15N]1.4-1.53
Sample conditionspH: 7.4 / Temperature: 313.4 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
PIPP3.5.6 to 3.9.9Delaglio, Zhengrong and Baxchemical shift assignment
PIPP3.5.6 to 3.9.9Delaglio, Zhengrong and Baxdata analysis
NMRPipe1.xDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
NMRPiperefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 90 / Conformers submitted total number: 1 / Representative conformer: 1

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