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- EMDB-60854: Cryo-EM structure of urease from Ureaplasma parvum -

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Basic information

Entry
Database: EMDB / ID: EMD-60854
TitleCryo-EM structure of urease from Ureaplasma parvum
Map data
Sample
  • Complex: Urease
    • Protein or peptide: Urease subunit gamma
    • Protein or peptide: Urease subunit beta
    • Protein or peptide: Urease subunit alpha
  • Ligand: BETA-MERCAPTOETHANOL
  • Ligand: NICKEL (II) ION
  • Ligand: water
Keywordsurease / 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 beta / Urease subunit gamma
Similarity search - Component
Biological speciesUreaplasma parvum serovar 3 (strain ATCC 700970) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.03 Å
AuthorsFujita J / Namba K / Wu HN / Yanagihara I
Funding support Japan, 7 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23fk0108677 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101117 and JP22ama121003 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121023 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Japan Science and TechnologyJPMJOP1861 Japan
The Research Foundation for Microbial Diseases, Osaka University Japan
JEOL YOKOGUSHI Research Alliance Laboratories of Osaka University Japan
CitationJournal: J Mol Biol / Year: 2025
Title: Structural Analysis and Molecular Dynamics Simulations of Urease From Ureaplasma parvum.
Authors: Heng Ning Wu / Junso Fujita / Yukiko Nakura / Masao Inoue / Koichiro Suzuki / Toru Ekimoto / Bingjie Yin / Yohta Fukuda / Kazuo Harada / Tsuyoshi Inoue / Mitsunori Ikeguchi / Keiichi Namba / Itaru Yanagihara /
Abstract: Ureaplasma is one of the smallest pathogenic bacteria, generating approximately 95% of its adenosine triphosphate (ATP) solely through urease. Studies on Ureaplasma parvum, a species of Ureaplasma, ...Ureaplasma is one of the smallest pathogenic bacteria, generating approximately 95% of its adenosine triphosphate (ATP) solely through urease. Studies on Ureaplasma parvum, a species of Ureaplasma, have confirmed that adding urease inhibitors inhibits bacterial growth. The K and V of the urease-mediated reaction were estimated to be 4.3 ± 0.2 mM and 3,333.3 ± 38.0 μmol NH/min/mg protein, respectively. The cryo-electron microscopy (cryo-EM) structure of Ureaplasma parvum urease (UPU) at a resolution of 2.03 Å reveals a trimer of heterotrimers comprising three proteins: UreA, UreB, and UreC. The active site is well conserved among the known ureases. However, the V of UPU was higher than that of most known ureases, including those ureases derived from Sporosarcina pasteurii (SPU) and Klebsiella aerogenes (KAU) with identical oligomeric state. All-atom molecular dynamics simulations showed that the flap and UreB are more open in UPU than SPU and KAU. His-tagged wild-type recombinant UPU (WT-rUPU) revealed estimated K and V values of 4.1 ± 0.3 mM and 769.2 ± 7.4 µmol NH/min/mg protein, respectively. Amino acid substitutions of recombinant UPUs within the flap region to SPU. Amongst the flap region variants, the V of K331N variant was 48-fold lower than that of WT-rUPU. ICP-MS analysis reveals that one molecule of UPU, WT-rUPU, and K331N-rUPU contains 3.7, 0.8, and 0.1 Ni atoms, respectively, suggesting that a wide-open flap of urease may contribute to delivering nickel into the enzyme, resulting in a high V. Ureaplasma evolved highly efficient UPU through a few amino acid substitutions in the disorganized loop of the mobile flap region.
History
DepositionJul 19, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60854.png

Downloads & links

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Map

FileDownload / File: emd_60854.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 314.28 Å		0.87 Å/pix.
x 360 pix.
= 314.28 Å		0.87 Å/pix.
x 360 pix.
= 314.28 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.873 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.5565683 - 2.9287658
Average (Standard dev.)0.00019595736 (±0.0657794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 314.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60854_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60854_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60854_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Urease

EntireName: Urease
Components
  • Complex: Urease
    • Protein or peptide: Urease subunit gamma
    • Protein or peptide: Urease subunit beta
    • Protein or peptide: Urease subunit alpha
  • Ligand: BETA-MERCAPTOETHANOL
  • Ligand: NICKEL (II) ION
  • Ligand: water

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Supramolecule #1: Urease

SupramoleculeName: Urease / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Ureaplasma parvum serovar 3 (strain ATCC 700970) (bacteria)

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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: Ureaplasma parvum serovar 3 (strain ATCC 700970) (bacteria)
Molecular weightTheoretical: 11.234106 KDa
SequenceString:
MNLSLREVQK LLITVAADVA RRRLARGLKL NYSEAVALIT DHVMEGARDG KLVADLMQSA REVLRVDQVM EGVDTMVSII QVEVTFPDG TKLVSVHDPI YK

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: Ureaplasma parvum serovar 3 (strain ATCC 700970) (bacteria)
Molecular weightTheoretical: 13.529323 KDa
SequenceString:
MSGSSSQFSP GKLVPGAINF ASGEIVMNEG REAKVISIKN TGDRPIQVGS HFHLFEVNSA LVFFDEKGNE DKERKVAYGR RFDIPSGTA IRFEPGDKKE VSIIDLAGTR EVWGVNGLVN GKLKK

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: Ureaplasma parvum serovar 3 (strain ATCC 700970) (bacteria)
Molecular weightTheoretical: 64.661324 KDa
SequenceString: MFKISRKNYS DLYGITTGDS VRLGDTNLWV KVEKDLTTYG EESVFGGGKT LREGMGMNST MKLDDKLGNA EVMDLVITNA LIVDYTGIY KADIGIKNGK IAAIGKSGNP HLTDNVDMIV GISTEISAGE GKIYTAGGLD THVHWLEPEI VPVALDGGIT T VIAGGTGM ...String:
MFKISRKNYS DLYGITTGDS VRLGDTNLWV KVEKDLTTYG EESVFGGGKT LREGMGMNST MKLDDKLGNA EVMDLVITNA LIVDYTGIY KADIGIKNGK IAAIGKSGNP HLTDNVDMIV GISTEISAGE GKIYTAGGLD THVHWLEPEI VPVALDGGIT T VIAGGTGM NDGTKATTVS PGKFWVKSAL QAADGLSINA GFLAKGQGME DPIFEQIAAG ACGL(KCX)IHEDW GATGNAID L ALTVADKTDV AVAIHTDTLN EAGFVEHTIA AMKGRTIHAY HTEGAGGGHA PDILETVKYA HILPASTNPT IPYTVNTIA EHLDMLMVCH HLNPKVPEDV AFADSRIRSQ TIAAEDLLHD MGAISIMSSD TLAMGRIGEV ATRTWQMAHK MKAQFGSLKG DSEFSDNNR VKRYISKYTI NPAIAHGVDS YIGSLEVGKL ADIVAWEPKF FGAKPYYVVK MGVIARCVAG DPNASIPTCE P VIMRDQFG TYGRLLTNTS VSFVSKIGLE NGIKEEYKLE KELLPVKNCR SVNKKSMKWN SATPNLEVDP QTFDAAVDFN DL ENWLEQS ASELAKKLKK TSSGKYILDA EPLTEAPLAQ RYFLF

UniProtKB: Urease subunit alpha

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Macromolecule #4: BETA-MERCAPTOETHANOL

MacromoleculeName: BETA-MERCAPTOETHANOL / type: ligand / ID: 4 / Number of copies: 3 / Formula: BME
Molecular weightTheoretical: 78.133 Da
Chemical component information

ChemComp-BME:
BETA-MERCAPTOETHANOL

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Macromolecule #5: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 434 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.78 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMTris-HClTris(hydroxymethyl)aminomethane
100.0 mMNaClsodium chloride
1.0 mM2-ME2-Mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 1.8 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3333272
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 207602
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-9it2:
Cryo-EM structure of urease from Ureaplasma parvum

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