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- EMDB-51478: Cryo-EM structure of Sporosarcina pasteurii urease inhibited by NBPTO -

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Basic information

Entry
Database: EMDB / ID: EMD-51478
TitleCryo-EM structure of Sporosarcina pasteurii urease inhibited by NBPTO
Map data
Sample
  • Organelle or cellular component: urease
    • Protein or peptide: Urease subunit gamma
    • Protein or peptide: Urease subunit beta
    • Protein or peptide: Urease subunit alpha
  • Ligand: NICKEL (II) ION
  • Ligand: DIAMIDOPHOSPHATE
Keywordsurease / urea / nickel / NBPTO / 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 speciesSporosarcina pasteurii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsMazzei L / Tria G / Ciurli S / Cianci M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Biol Macromol / Year: 2024
Title: Exploring the conformational space of the mobile flap in Sporosarcina pasteurii urease by cryo-electron microscopy.
Authors: Luca Mazzei / Giancarlo Tria / Stefano Ciurli / Michele Cianci /
Abstract: To fully understand enzymatic dynamics, it is essential to explore the complete conformational space of a biological catalyst. The catalytic mechanism of the nickel-dependent urease, the most ...To fully understand enzymatic dynamics, it is essential to explore the complete conformational space of a biological catalyst. The catalytic mechanism of the nickel-dependent urease, the most efficient enzyme known, holds significant relevance for medical, pharmaceutical, and agro-environmental applications. A critical aspect of urease function is the conformational change of a helix-turn-helix motif that covers the active site cavity, known as the mobile flap. This motif has been observed in either an open or a closed conformation through X-ray crystallography studies and has been proposed to stabilize the coordination of a urea molecule to the essential dinuclear Ni(II) cluster in the active site, a requisite for subsequent substrate hydrolysis. This study employs cryo-electron microscopy (cryo-EM) to investigate the transient states within the conformational space of the mobile flap, devoid of the possible constraints of crystallization conditions and solid-state effects. By comparing two cryo-EM structures of Sporosarcina pasteurii urease, one in its native form and the other inhibited by N-(n-butyl) phosphoric triamide (NBPTO), we have unprecedently identified an intermediate state between the open and the catalytically efficient closed conformation of the helix-turn-helix motif, suggesting a role of its tip region in this transition between the two states.
History
DepositionSep 3, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51478.png

Downloads & links

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Map

FileDownload / File: emd_51478.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.346709 - 0.7084688
Average (Standard dev.)0.0015562796 (±0.028206723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_51478_additional_1.map
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Half map: #2

Fileemd_51478_half_map_1.map
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Half map: #1

Fileemd_51478_half_map_2.map
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Sample components

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Entire : urease

EntireName: urease
Components
  • Organelle or cellular component: urease
    • Protein or peptide: Urease subunit gamma
    • Protein or peptide: Urease subunit beta
    • Protein or peptide: Urease subunit alpha
  • Ligand: NICKEL (II) ION
  • Ligand: DIAMIDOPHOSPHATE

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Supramolecule #1: urease

SupramoleculeName: urease / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Sporosarcina pasteurii (bacteria)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Urease subunit gamma

MacromoleculeName: Urease subunit gamma / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Sporosarcina pasteurii (bacteria)
Molecular weightTheoretical: 11.134895 KDa
SequenceString:
(CXM)HLNPAEKEK LQIFLASELA LKRKARGLKL NYPEAVAIIT SFIMEGARDG KTVAMLMEEG KHVLTRDDVM EGVPEM IDD IQAEATFPDG TKLVTVHNPI S

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: 1 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Sporosarcina pasteurii (bacteria)
Molecular weightTheoretical: 13.529061 KDa
SequenceString:
NYIVPGEYRV AEGEIEINAG REKTTIRVSN TGDRPIQVGS HIHFVEVNKE LLFDRAEGIG RRLNIPSGTA ARFEPGEEME VELTELGGN REVFGISDLT NGSVDNKELI LQRAKELGYK GVE

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: 1 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Sporosarcina pasteurii (bacteria)
Molecular weightTheoretical: 61.575648 KDa
SequenceString: MKINRQQYAE SYGPTVGDQV RLADTDLWIE VEKDYTTYGD EANFGGGKVL REGMGENGTY TRTENVLDLL LTNALILDYT GIYKADIGV KDGYIVGIGK GGNPDIMDGV TPNMIVGTAT EVIAAEGKIV TAGGIDTHVH FINPDQVDVA LANGITTLFG G GTGPAEGS ...String:
MKINRQQYAE SYGPTVGDQV RLADTDLWIE VEKDYTTYGD EANFGGGKVL REGMGENGTY TRTENVLDLL LTNALILDYT GIYKADIGV KDGYIVGIGK GGNPDIMDGV TPNMIVGTAT EVIAAEGKIV TAGGIDTHVH FINPDQVDVA LANGITTLFG G GTGPAEGS KATTVTPGPW NIEKMLKSTE GLPINVGILG KGHGSSIAPI MEQIDAGAAG L(KCX)IHEDWGAT PASIDRSL T VADEADVQVA IHSDTLNEAG FLEDTLRAIN GRVIHSFHVE GAGGGHAPDI MAMAGHPNVL PSSTNPTRPF TVNTIDEHL DMLMVCHHLK QNIPEDVAFA DSRIRPETIA AEDILHDLGI ISMMSTDALA MGRAGEMVLR TWQTADKMKK QRGPLAEEKN GSDNFRAKR YVSKYTINPA IAQGIAHEVG SIEEGKFADL VLWEPKFFGV KADRVIKGGI IAYAQIGDPS ASIPTPQPVM G RRMYGTVG DLIHDTNITF MSKSSIQQGV PAKLGLKRRI GTVKNCRNIG KKDMKWNDVT TDIDINPETY EVKVDGEVLT CE PVKELPM AQRYFLF

UniProtKB: Urease subunit alpha

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Macromolecule #4: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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Macromolecule #5: DIAMIDOPHOSPHATE

MacromoleculeName: DIAMIDOPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: 2PA
Molecular weightTheoretical: 96.026 Da
Chemical component information

ChemComp-2PA:
DIAMIDOPHOSPHATE

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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

Concentration2 mg/mL
BufferpH: 7.5
Details: 50 mM HEPES buffer, at pH 7.5, also containing 5 mM NBPTO
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 1459548 / Average exposure time: 3.2 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 163588
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9gnr:
Cryo-EM structure of Sporosarcina pasteurii urease inhibited by NBPTO

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