7FJL

Crystal Structure of phthalate dioxygenase from Comamonas testosteroni KF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular insights into substrate recognition and catalysis by phthalate dioxygenase from Comamonas testosteroni.

Mahto, J.K.Neetu, N.Waghmode, B.Kuatsjah, E.Sharma, M.Sircar, D.Sharma, A.K.Tomar, S.Eltis, L.D.Kumar, P.

(2021) J Biol Chem 297: 101416-101416

  • DOI: https://doi.org/10.1016/j.jbc.2021.101416
  • Primary Citation of Related Structures:  
    7FHR, 7FJL, 7V25, 7V28

  • PubMed Abstract: 

    Phthalate, a plasticizer, endocrine disruptor, and potential carcinogen, is degraded by a variety of bacteria. This degradation is initiated by phthalate dioxygenase (PDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of phthalate to a dihydrodiol. PDO has long served as a model for understanding ROs despite a lack of structural data. Here we purified PDO KF1 from Comamonas testosteroni KF1 and found that it had an apparent k cat /K m for phthalate of 0.58 ± 0.09 μM -1 s -1 , over 25-fold greater than for terephthalate. The crystal structure of the enzyme at 2.1 Å resolution revealed that it is a hexamer comprising two stacked α 3 trimers, a configuration not previously observed in RO crystal structures. We show that within each trimer, the protomers adopt a head-to-tail configuration typical of ROs. The stacking of the trimers is stabilized by two extended helices, which make the catalytic domain of PDO KF1 larger than that of other characterized ROs. Complexes of PDO KF1 with phthalate and terephthalate revealed that Arg207 and Arg244, two residues on one face of the active site, position these substrates for regiospecific hydroxylation. Consistent with their roles as determinants of substrate specificity, substitution of either residue with alanine yielded variants that did not detectably turnover phthalate. Together, these results provide critical insights into a pollutant-degrading enzyme that has served as a paradigm for ROs and facilitate the engineering of this enzyme for bioremediation and biocatalytic applications.


  • Organizational Affiliation

    Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rieske (2Fe-2S) domain protein
A, B, C, D, E
A, B, C, D, E, F
439Comamonas testosteroni KF-1Mutation(s): 0 
Gene Names: CtesDRAFT_PD2022
UniProt
Find proteins for B7WQT1 (Comamonas testosteroni (strain DSM 14576 / KF-1))
Explore B7WQT1 
Go to UniProtKB:  B7WQT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7WQT1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
DA [auth E]
H [auth A]
K [auth B]
LA [auth F]
S [auth C]
DA [auth E],
H [auth A],
K [auth B],
LA [auth F],
S [auth C],
X [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SRT
Query on SRT

Download Ideal Coordinates CCD File 
EA [auth E],
L [auth B],
MA [auth F],
T [auth C],
Y [auth D]
S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N
TLA
Query on TLA

Download Ideal Coordinates CCD File 
I [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth E]
FA [auth E]
GA [auth E]
HA [auth E]
AA [auth D],
BA [auth E],
FA [auth E],
GA [auth E],
HA [auth E],
IA [auth E],
JA [auth F],
M [auth B],
N [auth B],
NA [auth F],
O [auth B],
P [auth B],
Q [auth B],
U [auth C],
V [auth C],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
CA [auth E]
G [auth A]
J [auth B]
KA [auth F]
R [auth C]
CA [auth E],
G [auth A],
J [auth B],
KA [auth F],
R [auth C],
W [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.248α = 90
b = 121.375β = 100.95
c = 161.533γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
xia2data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/HRD/NBA/37/01/2015 (VIII)

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description