6DLL

2.2 Angstrom Resolution Crystal Structure of P-Hydroxybenzoate Hydroxylase from Pseudomonas putida in Complex with FAD.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural comparison of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida with PobA from other Pseudomonas spp. and other monooxygenases.

Lazar, J.T.Shuvalova, L.Rosas-Lemus, M.Kiryukhina, O.Satchell, K.J.F.Minasov, G.

(2019) Acta Crystallogr F Struct Biol Commun 75: 507-514

  • DOI: https://doi.org/10.1107/S2053230X19008653
  • Primary Citation of Related Structures:  
    6DLL

  • PubMed Abstract: 

    The crystal structure is reported of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida, a possible drug target to combat tetracycline resistance, in complex with flavin adenine dinucleotide (FAD). The structure was refined at 2.2 Å resolution with four polypeptide chains in the asymmetric unit. Based on the results of pairwise structure alignments, PobA from P. putida is structurally very similar to PobA from P. fluorescens and from P. aeruginosa. Key residues in the FAD-binding and substrate-binding sites of PobA are highly conserved spatially across the proteins from all three species. Additionally, the structure was compared with two enzymes from the broader class of oxygenases: 2-hydroxybiphenyl 3-monooxygenase (HbpA) from P. nitroreducens and 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) from Mesorhizobium japonicum. Despite having only 14% similarity in their primary sequences, pairwise structure alignments of PobA from P. putida with HbpA from P. nitroreducens and MHPCO from M. japonicum revealed local similarities between these structures. Key secondary-structure elements important for catalysis, such as the βαβ fold, β-sheet wall and α12 helix, are conserved across this expanded class of oxygenases.


  • Organizational Affiliation

    Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60201, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
p-hydroxybenzoate hydroxylase
A, B, C, D
398Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: pobAPP_3537
EC: 1.14.13.2
UniProt
Find proteins for Q88H28 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88H28 
Go to UniProtKB:  Q88H28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88H28
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
M [auth C],
Q [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
K [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]
H [auth B]
I [auth B]
J [auth B]
L [auth B]
F [auth A],
H [auth B],
I [auth B],
J [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth C],
R [auth D],
S [auth D],
T [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.041α = 90
b = 152.3β = 102.43
c = 88.636γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description