[English] 日本語
Yorodumi
- PDB-9it2: Cryo-EM structure of urease from Ureaplasma parvum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9it2
TitleCryo-EM structure of urease from Ureaplasma parvum
Components(Urease subunit ...) x 3
KeywordsHYDROLASE / urease
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
BETA-MERCAPTOETHANOL / NICKEL (II) ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesUreaplasma parvum serovar 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.03 Å
AuthorsFujita, J. / Namba, K. / Wu, H.N. / Yanagihara, I.
Funding support Japan, 7items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
D: Urease subunit gamma
E: Urease subunit beta
F: Urease subunit alpha
G: Urease subunit gamma
H: Urease subunit beta
I: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,86118
Polymers268,2749
Non-polymers5879
Water7,819434
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Urease subunit ... , 3 types, 9 molecules ADGBEHCFI

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


Mass: 11234.106 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Ureaplasma parvum serovar 3 (strain ATCC 700970) (bacteria)
References: UniProt: P0C7K9, urease
#2: Protein Urease subunit beta / Urea amidohydrolase subunit beta


Mass: 13529.323 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Ureaplasma parvum serovar 3 (strain ATCC 700970) (bacteria)
References: UniProt: P0C7K8, urease
#3: Protein Urease subunit alpha / Urea amidohydrolase subunit alpha


Mass: 64661.324 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Ureaplasma parvum serovar 3 (strain ATCC 700970) (bacteria)
References: UniProt: P0C7K7, urease

-
Non-polymers , 3 types, 443 molecules

#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Urease / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Ureaplasma parvum serovar 3 (strain ATCC 700970) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris(hydroxymethyl)aminomethaneTris-HCl1
2100 mMsodium chlorideNaCl1
31 mM2-Mercaptoethanol2-ME1
SpecimenConc.: 0.78 mg/ml / Embedding 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2SerialEM4image acquisition
4cryoSPARC4.2.1CTF correction
7UCSF Chimera1.15model fitting
9cryoSPARC4.2.1initial Euler assignment
10cryoSPARC4.2.1final Euler assignment
12cryoSPARC4.2.13D reconstruction
13PHENIX1.19.1-4122model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3333272
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207602 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00218972
ELECTRON MICROSCOPYf_angle_d0.51825671
ELECTRON MICROSCOPYf_dihedral_angle_d5.7252616
ELECTRON MICROSCOPYf_chiral_restr0.0442937
ELECTRON MICROSCOPYf_plane_restr0.0043312

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more