6E13

Pseudomonas putida PqqB with a non-physiological zinc at the active site binds the substrate mimic, 5-cysteinyl-3,4-dihydroxyphenylalanine (5-Cys-DOPA), non-specifically but supports the proposed function of the enzyme in pyrroloquinoline quinone biosynthesis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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This is version 1.1 of the entry. See complete history


Literature

Discovery of Hydroxylase Activity for PqqB Provides a Missing Link in the Pyrroloquinoline Quinone Biosynthetic Pathway.

Koehn, E.M.Latham, J.A.Armand, T.Evans 3rd, R.L.Tu, X.Wilmot, C.M.Iavarone, A.T.Klinman, J.P.

(2019) J Am Chem Soc 141: 4398-4405

  • DOI: https://doi.org/10.1021/jacs.8b13453
  • Primary Citation of Related Structures:  
    6E13

  • PubMed Abstract: 
  • Understanding the biosynthesis of cofactors is fundamental to the life sciences, yet to date a few important pathways remain unresolved. One example is the redox cofactor pyrroloquinoline quinone (PQQ), which is critical for C1 metabolism in many microorganisms, a disproportionate number of which are opportunistic human pathogens ...

    Understanding the biosynthesis of cofactors is fundamental to the life sciences, yet to date a few important pathways remain unresolved. One example is the redox cofactor pyrroloquinoline quinone (PQQ), which is critical for C1 metabolism in many microorganisms, a disproportionate number of which are opportunistic human pathogens. While the initial and final steps of PQQ biosynthesis, involving PqqD/E and PqqC, have been elucidated, the precise nature and order of the remaining transformations in the pathway are unknown. Here we show evidence that the remaining essential biosynthetic enzyme PqqB is an iron-dependent hydroxylase catalyzing oxygen-insertion reactions that are proposed to produce the quinone moiety of the mature PQQ cofactor. The demonstrated reactions of PqqB are unprecedented within the metallo β-lactamase protein family and expand the catalytic repertoire of nonheme iron hydroxylases. These new findings also generate a nearly complete description of the PQQ biosynthetic pathway.


    Organizational Affiliation

    Department of Molecular and Cell Biology , University of California-Berkeley , Berkeley , California 94720-3220 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coenzyme PQQ synthesis protein B308Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: pqqBPP_0379
EC: 1
UniProt
Find proteins for Q88QV5 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88QV5 
Go to UniProtKB:  Q88QV5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88QV5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HKS (Subject of Investigation/LOI)
Query on HKS

Download Ideal Coordinates CCD File 
E [auth A]3-{[(2S)-2-amino-2-carboxyethyl]sulfanyl}-5-hydroxy-L-tyrosine
C12 H16 N2 O6 S
SXISMOAILJWTID-NKWVEPMBSA-N
 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.038α = 90
b = 86.038β = 90
c = 107.128γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-66569
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-118117

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence