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- EMDB-17867: beta-Ureidopropionase tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-17867
Titlebeta-Ureidopropionase tetramer
Map data
Sample
  • Complex: beta-Ureidopropionase tetramer
    • Protein or peptide: Beta-ureidopropionase
KeywordsPyrimidine degradation / drug metabolism / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


pyrimidine nucleoside catabolic process / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase / beta-ureidopropionase activity / CMP catabolic process / dCMP catabolic process / UMP catabolic process / dUMP catabolic process / Pyrimidine catabolism / liver development ...pyrimidine nucleoside catabolic process / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase / beta-ureidopropionase activity / CMP catabolic process / dCMP catabolic process / UMP catabolic process / dUMP catabolic process / Pyrimidine catabolism / liver development / protein homooligomerization / in utero embryonic development / protein homotetramerization / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
: / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Beta-ureidopropionase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsCederfelt D / Dobritzsch D
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Carl Trygger FoundationCTS18:84 Sweden
CitationJournal: Biomolecules / Year: 2023
Title: The Allosteric Regulation of Β-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces.
Authors: Daniela Cederfelt / Dilip Badgujar / Ayan Au Musse / Bernhard Lohkamp / U Helena Danielson / Doreen Dobritzsch /
Abstract: The activity of β-ureidopropionase, which catalyses the last step in the degradation of uracil, thymine, and analogous antimetabolites, is cooperatively regulated by the substrate and product of the ...The activity of β-ureidopropionase, which catalyses the last step in the degradation of uracil, thymine, and analogous antimetabolites, is cooperatively regulated by the substrate and product of the reaction. This involves shifts in the equilibrium of the oligomeric states of the enzyme, but how these are achieved and result in changes in enzyme catalytic competence has yet to be determined. Here, the regulation of human β-ureidopropionase was further explored via site-directed mutagenesis, inhibition studies, and cryo-electron microscopy. The active-site residue E207, as well as H173 and H307 located at the dimer-dimer interface, are shown to play crucial roles in enzyme activation. Dimer association to larger assemblies requires closure of active-site loops, which positions the catalytically crucial E207 stably in the active site. H173 and H307 likely respond to ligand-induced changes in their environment with changes in their protonation states, which fine-tunes the active-site loop stability and the strength of dimer-dimer interfaces and explains the previously observed pH influence on the oligomer equilibrium. The correlation between substrate analogue structure and effect on enzyme assembly suggests that the ability to favourably interact with F205 may distinguish activators from inhibitors. The cryo-EM structure of human β-ureidopropionase assembly obtained at low pH provides first insights into the architecture of its activated state. and validates our current model of the allosteric regulation mechanism. Closed entrance loop conformations and dimer-dimer interfaces are highly conserved between human and fruit fly enzymes.
History
DepositionJul 13, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17867.png

Downloads & links

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Map

FileDownload / File: emd_17867.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 329.6 Å		0.82 Å/pix.
x 400 pix.
= 329.6 Å		0.82 Å/pix.
x 400 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.039
Minimum - Maximum-0.26126447 - 0.47063705
Average (Standard dev.)0.0003859674 (±0.010371508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 329.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17867_half_map_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_17867_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 : beta-Ureidopropionase tetramer

EntireName: beta-Ureidopropionase tetramer
Components
  • Complex: beta-Ureidopropionase tetramer
    • Protein or peptide: Beta-ureidopropionase

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Supramolecule #1: beta-Ureidopropionase tetramer

SupramoleculeName: beta-Ureidopropionase tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 430 KDa

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Macromolecule #1: Beta-ureidopropionase

MacromoleculeName: Beta-ureidopropionase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: beta-ureidopropionase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.218965 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGAEWKSLE ECLEKHLPLP DLQEVKRVLY GKELRKLDLP REAFEAASRE DFELQGYAFE AAEEQLRRPR IVHVGLVQNR IPLPANAPV AEQVSALHRR IKAIVEVAAM CGVNIICFQE AWTMPFAFCT REKLPWTEFA ESAEDGPTTR FCQKLAKNHD M VVVSPILE ...String:
MAGAEWKSLE ECLEKHLPLP DLQEVKRVLY GKELRKLDLP REAFEAASRE DFELQGYAFE AAEEQLRRPR IVHVGLVQNR IPLPANAPV AEQVSALHRR IKAIVEVAAM CGVNIICFQE AWTMPFAFCT REKLPWTEFA ESAEDGPTTR FCQKLAKNHD M VVVSPILE RDSEHGDVLW NTAVVISNSG AVLGKTRKNH IPRVGDFNES TYYMEGNLGH PVFQTQFGRI AVNICYGRHH PL NWLMYSI NGAEIIFNPS ATIGALSESL WPIEARNAAI ANHCFTCAIN RVGTEHFPNE FTSGDGKKAH QDFGYFYGSS YVA APDSSR TPGLSRSRDG LLVAKLDLNL CQQVNDVWNF KMTGRYEMYA RELAEAVKSN YSPTIVKE

UniProtKB: Beta-ureidopropionase

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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

Concentration1 mg/mL
BufferpH: 5
Component:
ConcentrationFormulaName
100.0 mMC2H3NaO2Sodium acetate
50.0 mMNaClSodium chloride

Details: 100 mM sodium acetate, 50 mM sodium chloride, pH 5.0
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.661 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: AlphaFold structure for HsbUP and PDB entry 6FTQ
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Number images used: 169949
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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