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- PDB-9i2q: Wzc-K540M-3YE MgADP C1 -

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Basic information

Entry
Database: PDB / ID: 9i2q
TitleWzc-K540M-3YE MgADP C1
ComponentsPutative transmembrane protein Wzc
KeywordsMEMBRANE PROTEIN / Wzc-K540M-3YE
Function / homology
Function and homology information


protein tyrosine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase Wzc, N-terminal domain / Tyrosine kinase, G-rich domain / G-rich domain on putative tyrosine kinase / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / : / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Putative transmembrane protein Wzc
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLiu, J.W. / Yang, Y. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis for the phosphorylation of bacterial tyrosine kinase Wzc.
Authors: Yun Yang / Mariana Batista / Bradley R Clarke / Michelle R Agyare-Tabbi / Haigang Song / Noah M Kuehfuss / Audrey Le Bas / Carol V Robinson / Chris Whitfield / Phillip J Stansfeld / James H ...Authors: Yun Yang / Mariana Batista / Bradley R Clarke / Michelle R Agyare-Tabbi / Haigang Song / Noah M Kuehfuss / Audrey Le Bas / Carol V Robinson / Chris Whitfield / Phillip J Stansfeld / James H Naismith / Jiwei Liu /
Abstract: The regulation of polymerisation and translocation of biomolecules is fundamental. Wzc, an integral cytoplasmic membrane tyrosine autokinase protein serves as the master regulator of the biosynthesis ...The regulation of polymerisation and translocation of biomolecules is fundamental. Wzc, an integral cytoplasmic membrane tyrosine autokinase protein serves as the master regulator of the biosynthesis and export of many bacterial capsular polysaccharides and exopolysaccharides. Such polysaccharides play essential roles in infection, defence, and some are important industrial products. Wzc comprises a large periplasmic domain, two transmembrane helices and a C-terminal cytoplasmic kinase domain with a tyrosine-rich tail. Wzc regulates polymerisation functions through cycling the formation and dissociation of an octameric complex, driven by changes in the phosphorylation status of the tyrosine-rich tail. E. coli Wzc serves a model for a wider family of polysaccharide co-polymerases. Here, we determine structures of intermediate states with different extents of phosphorylation. Structural and computational data reveal the pre-ordering of the tyrosine-rich tail, the molecular basis underlying the unidirectionality of phosphorylation events, and the underlying structural dynamics on how phosphorylation status is transmitted.
History
DepositionJan 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Putative transmembrane protein Wzc
E: Putative transmembrane protein Wzc
F: Putative transmembrane protein Wzc
G: Putative transmembrane protein Wzc
H: Putative transmembrane protein Wzc
A: Putative transmembrane protein Wzc
B: Putative transmembrane protein Wzc
C: Putative transmembrane protein Wzc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)647,36524
Polymers643,7538
Non-polymers3,61216
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Putative transmembrane protein Wzc


Mass: 80469.164 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: wzc / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X4B9
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Wzc-K540M-3YE / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 38.3 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 519340 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00436401
ELECTRON MICROSCOPYf_angle_d0.56649325
ELECTRON MICROSCOPYf_dihedral_angle_d11.70913649
ELECTRON MICROSCOPYf_chiral_restr0.0455937
ELECTRON MICROSCOPYf_plane_restr0.0056281

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