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 9US2 | pdb_00009us2

Crystal structure of YgdH from Neisseria meningitidis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.229 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9US2

This is version 1.1 of the entry. See complete history. 

Literature

A combined pseudouridine biomanufacturing platform enabled by a streamlined designer pathway.

Yu, L., Chen, R., Zhang, C., Wang, Z., Wang, Z., Zeng, X., Liang, H., He, Y., She, Y., Wang, Y., Gong, R., Song, X., Deng, Z., Fei, Q., Chen, W.

(2025) Nat Commun 16: 8866-8866

  • DOI: https://doi.org/10.1038/s41467-025-63906-0
  • Primary Citation Related Structures: 
    9US2

  • PubMed Abstract: 

    mRNA vaccines, featured by incorporated pseudouridine (Ψ), represent a milestone in combating diseases, thus highlighting Ψ importance in drug development. However, economic and environmental challenges have persisted in sustainable Ψ production. Here, we formulate a streamlined designer Ψ pathway, comprising UMP nucleosidase, ΨMP glycosidase, and ΨMP phosphatase, and realize its gram-scale production by targeted discovery of a prominent UMP-preferred nucleosidase (NmYgdH). The optimized pathway, containing NmYgdH, RjPsuG (ΨMP glycosidase), and HDHD1 (ΨMP-specific phosphatase) is cloned into E. coli and systematic evaluation of multiple strategies achieves a Ψ titer of 44.8 g·L -1 . Moreover, a thyA-dependent, tunable, and eco-friendly strategy for sustainable Ψ production is demonstrated in a 5 L bioreactor achieving titer of 45.3 g·L -1 . Finally, we establish a simplified-strategy for rapid Ψ purification with a recovery-rate of 71%, and techno-economic analysis is employed to validate the feasibility and advantages of this fermentation platform for Ψ biomanufacturing. Therefore, this study provides a blueprint for industrial-production of nucleoside-related molecules.


  • Organizational Affiliation: 
    • Department of Anesthesiology, Zhongnan Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.

Macromolecule Content 

  • Total Structure Weight: 68.33 kDa 
  • Atom Count: 4,895 
  • Modeled Residue Count: 612 
  • Deposited Residue Count: 630 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytokinin riboside 5'-monophosphate phosphoribohydrolase
A, B, C
210Neisseria meningitidisMutation(s): 0 
Gene Names: ygdH, CNQ34_05655, COI09_06730, DE8555_0277, ERS514591_00967, ERS514851_00315
EC: 3.2.2
UniProt
Find proteins for Q9K184 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58))
Explore Q9K184 
Go to UniProtKB:  Q9K184
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K184
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT

Query on CIT



Download:Ideal Coordinates CCD File
D [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.229 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.814α = 90
b = 142.236β = 90
c = 119.308γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32170026
National Natural Science Foundation of China (NSFC)China32470047

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references