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- PDB-8hcn: CryoEM Structure of Klebsiella pneumoniae UreD/urease complex -

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Basic information

Entry
Database: PDB / ID: 8hcn
TitleCryoEM Structure of Klebsiella pneumoniae UreD/urease complex
Components
  • Urease accessory protein UreD
  • Urease subunit alpha
  • Urease subunit beta
  • Urease subunit gamma
KeywordsHYDROLASE / Urease / UreA / UreB / UreC / UreF / UreD / Klebsiella pneumoniae
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, gamma subunit / : / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily ...Urease, gamma subunit / : / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / : / Urease, gamma subunit / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Urease subunit alpha / Urease subunit gamma / : / Urease subunit beta
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsNim, Y.S. / Fong, I.Y.H. / Deme, J. / Tsang, K.L. / Caesar, J. / Johnson, S. / Wong, K.B. / Lea, S.M.
Funding support Hong Kong, United States, United Kingdom, 4items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)C4041-18E, C4033-19EF, C4012-16E, 14117321, AoE/M-403/16, AoE/M-05/12 Hong Kong
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Wellcome Trust219477 United Kingdom
Medical Research Council (MRC, United Kingdom)S021264 United Kingdom
CitationJournal: Sci Adv / Year: 2023
Title: Delivering a toxic metal to the active site of urease.
Authors: Yap Shing Nim / Ivan Yu Hang Fong / Justin Deme / Ka Lung Tsang / Joseph Caesar / Steven Johnson / Longson Tsz Hin Pang / Nicholas Man Hon Yuen / Tin Long Chris Ng / Tung Choi / Yakie Yat ...Authors: Yap Shing Nim / Ivan Yu Hang Fong / Justin Deme / Ka Lung Tsang / Joseph Caesar / Steven Johnson / Longson Tsz Hin Pang / Nicholas Man Hon Yuen / Tin Long Chris Ng / Tung Choi / Yakie Yat Hei Wong / Susan M Lea / Kam-Bo Wong /
Abstract: Urease is a nickel (Ni) enzyme that is essential for the colonization of in the human stomach. To solve the problem of delivering the toxic Ni ion to the active site without diffusing into the ...Urease is a nickel (Ni) enzyme that is essential for the colonization of in the human stomach. To solve the problem of delivering the toxic Ni ion to the active site without diffusing into the cytoplasm, cells have evolved metal carrier proteins, or metallochaperones, to deliver the toxic ions to specific protein complexes. Ni delivery requires urease to form an activation complex with the urease accessory proteins UreFD and UreG. Here, we determined the cryo-electron microscopy structures of UreFD/urease and UreD/urease complexes at 2.3- and 2.7-angstrom resolutions, respectively. Combining structural, mutagenesis, and biochemical studies, we show that the formation of the activation complex opens a 100-angstrom-long tunnel, where the Ni ion is delivered through UreFD to the active site of urease.
History
DepositionNov 2, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
D: Urease accessory protein UreD
E: Urease subunit gamma
F: Urease subunit beta
G: Urease subunit alpha
H: Urease accessory protein UreD
I: Urease subunit gamma
J: Urease subunit beta
K: Urease subunit alpha
L: Urease accessory protein UreD


Theoretical massNumber of molelcules
Total (without water)343,32412
Polymers343,32412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Urease subunit gamma / Urea amidohydrolase subunit gamma


Mass: 11100.928 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W8AWT7, urease
#2: Protein Urease subunit beta / Urea amidohydrolase subunit beta


Mass: 11712.239 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W9BBU3, urease
#3: Protein Urease subunit alpha / Urea amidohydrolase subunit alpha


Mass: 60352.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: ureC, ureC_1, DDJ63_24795, NCTC13443_06457, NCTC5052_03970, SAMEA3649733_03670, SAMEA3727643_03166
Production host: Escherichia coli (E. coli) / References: UniProt: A0A060VJP5, urease
#4: Protein Urease accessory protein UreD


Mass: 31275.982 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ureD, DDJ63_24810 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5D6SRX8

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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: Klebsiella pneumoniae UreD/urease complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.36 MDa / Experimental value: NO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -1500 nm / Nominal defocus min: -500 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89857 / Symmetry type: POINT

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