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- EMDB-34659: CryoEM Structure of Klebsiella pneumoniae UreD/urease complex -

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Basic information

Entry
Database: EMDB / ID: EMD-34659
TitleCryoEM Structure of Klebsiella pneumoniae UreD/urease complex
Map data
Sample
  • Complex: Klebsiella pneumoniae UreD/urease complex
    • Protein or peptide: Urease subunit gamma
    • Protein or peptide: Urease subunit beta
    • Protein or peptide: Urease subunit alpha
    • Protein or peptide: Urease accessory protein UreD
KeywordsUrease / UreA / UreB / UreC / UreF / UreD / Klebsiella pneumoniae / HYDROLASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsNim YS / Fong IYH / Deme J / Tsang KL / Caesar J / Johnson S / Wong KB / Lea SM
Funding support Hong Kong, United States, United Kingdom, 4 items
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, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34659.png

Downloads & links

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Map

FileDownload / File: emd_34659.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246.6 Å		0.82 Å/pix.
x 300 pix.
= 246.6 Å		0.82 Å/pix.
x 300 pix.
= 246.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0022101
Minimum - Maximum-0.016913284 - 0.0501147
Average (Standard dev.)0.00003967965 (±0.0022101093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34659_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34659_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Klebsiella pneumoniae UreD/urease complex

EntireName: Klebsiella pneumoniae UreD/urease complex
Components
  • Complex: Klebsiella pneumoniae UreD/urease complex
    • Protein or peptide: Urease subunit gamma
    • Protein or peptide: Urease subunit beta
    • Protein or peptide: Urease subunit alpha
    • Protein or peptide: Urease accessory protein UreD

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Supramolecule #1: Klebsiella pneumoniae UreD/urease complex

SupramoleculeName: Klebsiella pneumoniae UreD/urease complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: Urease subunit gamma

MacromoleculeName: Urease subunit gamma / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 11.100928 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MELTPREKDK LLLFTAALVA ERRLARGLKL NYPESVALIS AFIMEGARDG KSVASLMEEG RHVLTREQVM EGVPEMIPDI QVEATFPDG SKLVTVHNPI I

UniProtKB: Urease subunit gamma

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Macromolecule #2: Urease subunit beta

MacromoleculeName: Urease subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 11.712239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIPGEYHVKP GQIALNTGRA TCRVVVENHG DRPIQVGSHY HFAEVNPALK FDRQQAAGYR LNIPAGTAVR FEPGQKREVE LVAFAGHRA VFGFRGEVMG PLEVNDE

UniProtKB: Urease subunit beta

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Macromolecule #3: Urease subunit alpha

MacromoleculeName: Urease subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 60.352328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNISRQAYA DMFGPTVGDK VRLADTELWI EVEDDLTTYG EEVKFGGGKV IRDGMGQGQM LAADCVDLVL TNALIVDHWG IVKADIGVK DGRIFAIGKA GNPDIQPNVT IPIGAATEVI AAEGKIVTAG GIDTHIHWIC PQQAEEALVS GVTTMVGGGT G PAAGTHAT ...String:
MSNISRQAYA DMFGPTVGDK VRLADTELWI EVEDDLTTYG EEVKFGGGKV IRDGMGQGQM LAADCVDLVL TNALIVDHWG IVKADIGVK DGRIFAIGKA GNPDIQPNVT IPIGAATEVI AAEGKIVTAG GIDTHIHWIC PQQAEEALVS GVTTMVGGGT G PAAGTHAT TCTPGPWYIS RMLQAADSLP VNIGLLGKGN VSQPDALREQ VAAGVIGLKI HEDWGATPAA IDCALTVADE MD VQVALHS DTLNESGFVE DTLAAIGGRT IHTFHTEGAG GGHAPDIITA CAHPNILPSS TNPTLPYTLN TIDEHLDMLM VCH HLDPDI AEDVAFAESR IRRETIAAED VLHDLGAFSL TSSDSQAMGR VGEVILRTWQ VAHRMKVQRG ALAEETGDND NFRV KRYIA KYTINPALTH GIAHEVGSIE VGKLADLVVW SPAFFGVKPA TVIKGGMIAI APMGDINASI PTPQPVHYRP MFGAL GSAR HHCRLTFLSQ AAAANGVAER LNLRSAIAVV KGCRTVQKAD MVHNSLQPNI TVDAQTYEVR VDGELITSEP ADVLPM AQR YFLF

UniProtKB: Urease subunit alpha

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Macromolecule #4: Urease accessory protein UreD

MacromoleculeName: Urease accessory protein UreD / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 31.275982 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWSHPQFEKH GTVLPPLKKG WQATLDLRFH QAGGKTVLAS AQHVGPLTVQ RPFYPEEETC HLYLLHPPGG IVGGDELTIS AQLAPGCHT LITMPGASKF YRSSGAQALV RQQLTLAPQA TLEWLPQDAI FFPGANARLF TTFHLCASSR LLAWDLLCLG R PVIGETFS ...String:
MWSHPQFEKH GTVLPPLKKG WQATLDLRFH QAGGKTVLAS AQHVGPLTVQ RPFYPEEETC HLYLLHPPGG IVGGDELTIS AQLAPGCHT LITMPGASKF YRSSGAQALV RQQLTLAPQA TLEWLPQDAI FFPGANARLF TTFHLCASSR LLAWDLLCLG R PVIGETFS HGTLSNRLEV WVDDEPLLVE RLQLQEGELS SVAERPWVGT LLCYPATDAL LDGVRDALAP LGLYAGASLT DR LLTVRFL SDDNLICQRV MRDVWQFLRP HLTGKSPVLP RIWLT

UniProtKB: UNIPROTKB: A0A5D6SRX8

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -1.5 µm / Nominal defocus min: -0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1kra

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89857
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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