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- PDB-2lp4: Solution structure of P1-CheY/P2 complex in bacterial chemotaxis -

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Basic information

Entry
Database: PDB / ID: 2lp4
TitleSolution structure of P1-CheY/P2 complex in bacterial chemotaxis
Components
  • Chemotaxis protein CheA
  • Chemotaxis protein CheY
KeywordsTRANSFERASE/SIGNALING PROTEIN / Two Component Signaling system / Histidine phosphotransfer domain / Response Regulator / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


negative regulation of protein modification process / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity / bacterial-type flagellum ...negative regulation of protein modification process / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity / bacterial-type flagellum / histidine phosphotransfer kinase activity / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / histidine kinase / phosphorelay signal transduction system / phosphorelay sensor kinase activity / acetyltransferase activity / establishment of localization in cell / chemotaxis / phosphorylation / magnesium ion binding / signal transduction / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CheY-binding domain of CheA / CheY binding / CheY binding / HPT domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. ...CheY-binding domain of CheA / CheY binding / CheY binding / HPT domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Alpha-Beta Plaits / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheA / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsDahlquist, F. / Mo, G. / Zhou, H. / Kamamura, T.
CitationJournal: Biochemistry / Year: 2012
Title: Solution structure of a complex of the histidine autokinase CheA with its substrate CheY.
Authors: Mo, G. / Zhou, H. / Kawamura, T. / Dahlquist, F.W.
History
DepositionJan 31, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemotaxis protein CheA
Y: Chemotaxis protein CheY


Theoretical massNumber of molelcules
Total (without water)38,9722
Polymers38,9722
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chemotaxis protein CheA


Mass: 24990.848 Da / Num. of mol.: 1 / Fragment: 1-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cheA, b1888, JW1877 / Production host: Escherichia coli (E. coli) / References: UniProt: P07363, histidine kinase
#2: Protein Chemotaxis protein CheY


Mass: 13981.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cheY, b1882, JW1871 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AE67
Sequence detailsTHE AUTHOR STATES THAT SINCE AN E.COLI P1 STRUCTURE IS NOT AVAILABLE, THEIR STARTING STRUCTURE WAS ...THE AUTHOR STATES THAT SINCE AN E.COLI P1 STRUCTURE IS NOT AVAILABLE, THEIR STARTING STRUCTURE WAS GENERATED BY LINKING THE SALMONELLA TYPHIMURIUM P1 (1I5N) AND E. COLI CHEY/P2 (1EAY), AND THEY WERE REFINED USING THE EXPERIMENTAL CONSTRAINTS THEY OBTAINED USING THE E.COLI P1. THE P1 PART OF THE MODELS THEY DEPOSITED, THEREFORE, IS THE SALMONELLA P1, AND THESE CONFLICTS REFLECT THE DIFFERENCES IN SEQUENCE IN SALMONELLA P1 (2LP4) AND E. COLI P1.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 200 mM [U-15N; U-2H] CheY, 3000 mM [U-2H] CheA P1, 250 mM [U-2H] CheA P2, 92% H2O/8% D2O
Solvent system: 92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 mMCheY-1[U-15N; U-2H]1
3000 mMCheA P1-2[U-2H]1
250 mMCheA P2-3[U-2H]1
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ANSIG3.3Kraulischemical shift assignment
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE AUTHORS STATE THAT THE STRUCTURE CALCULATION USED X-RAY STRUCTURES SALMONELLA TYPHIMURIUM P1 (1I5N) AND E. COLI CHEY/P2 (1EAY). THEY WERE CONFINED AS RIGID BODIES EXCEPT FOR THE DOMAIN ...Details: THE AUTHORS STATE THAT THE STRUCTURE CALCULATION USED X-RAY STRUCTURES SALMONELLA TYPHIMURIUM P1 (1I5N) AND E. COLI CHEY/P2 (1EAY). THEY WERE CONFINED AS RIGID BODIES EXCEPT FOR THE DOMAIN LINKERS. THE PROGRAM XPLOR-NIH WAS USED TO REFINE THE STRUCTURES.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25

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