9Y0P | pdb_00009y0p

Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

A universal cis-proline lock defines catalysis in thioredoxin-fold enzymes.

Cunliffe, T.Wang, G.Penning, S.Subedi, P.Totsika, M.Paxman, J.J.Heras, B.

(2026) Commun Biol 

  • DOI: https://doi.org/10.1038/s42003-026-10010-8
  • Primary Citation Related Structures: 
    9Y0M, 9Y0N, 9Y0O, 9Y0P, 9Y0Q

  • PubMed Abstract: 

    Thioredoxin-fold oxidoreductases drive oxidative protein folding and redox homeostasis across all domains of life. They catalyse thiol-disulfide exchange in diverse substrates, yet how they reconcile catalytic precision with substrate diversity remains unclear. Here we show, using high-resolution structures and functional analyses of the Escherichia coli oxidoreductase DsbA, that a conserved cis-proline loop adjacent to the catalytic Cys-Pro-His-Cys motif serves as a universal catalytic lock. The loop positions the substrate cysteine in a right-handed disulfide geometry optimal for exchange, while surrounding surfaces accommodate sequence variation. Substitution of the cis-proline abolishes turnover, whereas mutation of the preceding glycine preserves geometry but reduces efficiency. Comparative structural analyses demonstrate that this cis-proline-dependent hydrogen-bonding scaffold is conserved across thioredoxins, protein disulfide isomerases, peroxiredoxins and bacterial Dsb proteins. This conserved mechanism explains how catalytic fidelity is maintained while enabling substrate versatility and provides a foundation for enzyme engineering and therapeutic development.


  • Organizational Affiliation
    • Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia.

Macromolecule Content 

  • Total Structure Weight: 45.6 kDa 
  • Atom Count: 3,623 
  • Modeled Residue Count: 399 
  • Deposited Residue Count: 408 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thiol:disulfide interchange protein DsbAA,
B [auth C]
190Escherichia coli K-12Mutation(s): 1 
Gene Names: dsbAdsfppfAb3860JW3832
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12))
Explore P0AEG4 
Go to UniProtKB:  P0AEG4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEG4
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide from LPS-assembly protein LptDC [auth D],
D [auth B]
14Escherichia coliMutation(s): 2 
UniProt
Find proteins for P31554 (Escherichia coli (strain K12))
Explore P31554 
Go to UniProtKB:  P31554
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31554
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
L [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3

Query on NO3



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
J [auth A],
K [auth C],
M [auth C]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.21α = 90
b = 79.335β = 90
c = 82.503γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP190101613
Australian Research Council (ARC)AustraliaDP210100673
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1144046

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release
  • Version 1.1: 2026-04-29
    Changes: Database references