Crystal structure of the pyoverdine maturation protein PvdP in complex with the mock substrates L-tyrosine and zinc.

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.210 

Starting Model: experimental
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Pseudomonas aeruginosapyoverdine maturation enzyme PvdP has a noncanonical domain architecture and affords insight into a new subclass of tyrosinases.

Poppe, J.Reichelt, J.Blankenfeldt, W.

(2018) J Biol Chem 293: 14926-14936

  • DOI: https://doi.org/10.1074/jbc.RA118.002560
  • Primary Citation of Related Structures:  
    6EYS, 6EYV

  • PubMed Abstract: 

    Pyoverdines (PVDs) are important chromophore-containing siderophores of fluorescent pseudomonad bacteria such as the opportunistic human pathogen Pseudomonas aeruginosa in which they play an essential role in host infection. PVD biosynthesis encompasses a complex pathway comprising cytosolic nonribosomal peptide synthetases that produce a polypeptide precursor that periplasmic enzymes convert to the final product. The structures of most enzymes involved in PVD chromophore maturation have been elucidated, but the structure of the essential tyrosinase PvdP, a monooxygenase required for the penultimate step in PVD biosynthesis, is not known. Here, we closed this gap by determining the crystal structure of PvdP in an apo and tyrosine-complexed state at 2.1 and 2.7 Å, respectively. These structures revealed that PvdP is a homodimer, with each chain consisting of a C-terminal tyrosinase domain and an N-terminal eight-stranded β-barrel reminiscent of streptavidin that appears to have a structural role only. We observed that ligand binding leads to the displacement of a "placeholder" tyrosine that blocks the active site in the apo structure. This exposes a large, deep binding site that seems suitable for accommodating ferribactin, a substrate of PvdP in PVD biosynthesis. The binding site consists almost exclusively of residues from the tyrosinase domain. Of note, we also found that this domain is more closely related to tyrosinases from arthropods rather than to tyrosinases from other bacteria. In conclusion, our work unravels the structural basis of PvdP's activity in PVD biosynthesis, observations that may inform structure-guided development of PvdP-specific inhibitors to manage P. aeruginosa infections.

  • Organizational Affiliation

    From the Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PvdPA [auth B],
B [auth A]
536Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: pvdPPA14_33740
Find proteins for A0A0H2ZBG1 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2ZBG1 
Go to UniProtKB:  A0A0H2ZBG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZBG1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.332α = 90
b = 109.143β = 95.66
c = 82.51γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
STARANISOdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description