Crystal Structure of PqqC Active Site Mutant H154S in Complex with PQQ

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural studies of mutant forms of the PQQ-forming enzyme PqqC in the presence of product and substrate

Puehringer, S.RoseFigura, J.Metlitzky, M.Toyama, H.Klinman, J.P.Schwarzenbacher, R.

(2010) Proteins 78: 2554-2562

  • DOI: https://doi.org/10.1002/prot.22769
  • Primary Citation of Related Structures:  
    3HLX, 3HML, 3HNH

  • PubMed Abstract: 

    Pyrroloquinoline quinone [4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid (PQQ)] is a bacterial cofactor in numerous alcohol dehydrogenases including methanol dehydrogenase and glucose dehydrogenase. Its biosynthesis in Klebsiella pneumoniae is facilitated by six genes, pqqABCDEF and proceeds by an unknown pathway. PqqC is one of two metal free oxidases of known structure and catalyzes the last step of PQQ biogenesis which involves a ring closure and an eight-electron oxidation of the substrate [3a-(2-amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline-7,9-dicarboxylic acid (AHQQ)]. PqqC has 14 conserved active site residues, which have previously been shown to be in close contact with bound PQQ. Herein, we describe the structures of three PqqC active site variants, H154S, Y175F, and the double mutant R179S/Y175S. The H154S crystal structure shows that, even with PQQ bound, the enzyme is still in the "open" conformation with helices alpha5b and alpha6 unfolded and the active site solvent accessible. The Y175F PQQ complex crystal structure reveals the closed conformation indicating that Y175 is not required for the conformational change. The R179S/Y175S AHQQ complex crystal structure is the most mechanistically informative, indicating an open conformation with a reaction intermediate trapped in the active site. The intermediate seen in R179S/Y175S is tricyclic but nonplanar, implying that it has not undergone oxidation. These studies implicate a stepwise process in which substrate binding leads to the generation of the closed protein conformation, with the latter playing a critical role in O(2) binding and catalysis.

  • Organizational Affiliation

    Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrroloquinoline-quinone synthase
A, B
258Klebsiella pneumoniae subsp. pneumoniae MGH 78578Mutation(s): 1 
Gene Names: pqqC
Find proteins for A6T9H1 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6T9H1 
Go to UniProtKB:  A6T9H1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6T9H1
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.06α = 90
b = 118.291β = 90
c = 68.04γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-04
    Changes: Data collection
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description