7Q05

Crystal structure of TPADO in complex with TPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Biochemical and structural characterization of an aromatic ring-hydroxylating dioxygenase for terephthalic acid catabolism.

Kincannon, W.M.Zahn, M.Clare, R.Lusty Beech, J.Romberg, A.Larson, J.Bothner, B.Beckham, G.T.McGeehan, J.E.DuBois, J.L.

(2022) Proc Natl Acad Sci U S A 119: e2121426119-e2121426119

  • DOI: https://doi.org/10.1073/pnas.2121426119
  • Primary Citation of Related Structures:  
    7Q04, 7Q05, 7Q06

  • PubMed Abstract: 

    SignificanceMore than 400 million tons of plastic waste is produced each year, the overwhelming majority of which ends up in landfills. Bioconversion strategies aimed at plastics have emerged as important components of enabling a circular economy for synthetic plastics, especially those that exhibit chemically similar linkages to those found in nature, such as polyesters. The enzyme system described in this work is essential for mineralization of the xenobiotic components of poly(ethylene terephthalate) (PET) in the biosphere. Our description of its structure and substrate preferences lays the groundwork for in vivo or ex vivo engineering of this system for PET upcycling.


  • Organizational Affiliation

    Department of Biochemistry, Montana State University, Bozeman, MT 59717.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1
A, B, C
154Comamonas sp.Mutation(s): 0 
Gene Names: tphA3I
EC: 1.14.12.15
UniProt
Find proteins for Q3C1E2 (Comamonas sp)
Explore Q3C1E2 
Go to UniProtKB:  Q3C1E2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3C1E2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2
D, E, F
428Comamonas sp.Mutation(s): 0 
Gene Names: tphA2II
EC: 1.14.12.15
UniProt
Find proteins for Q3C1D5 (Comamonas sp)
Explore Q3C1D5 
Go to UniProtKB:  Q3C1D5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3C1D5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
LysozymeG [auth H]129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
H [auth D],
M [auth E],
T [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
UB7 (Subject of Investigation/LOI)
Query on UB7

Download Ideal Coordinates CCD File 
K [auth D],
R [auth E],
W [auth F]
terephthalic acid
C8 H6 O4
KKEYFWRCBNTPAC-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
I [auth D]
J [auth D]
N [auth E]
O [auth E]
P [auth E]
I [auth D],
J [auth D],
N [auth E],
O [auth E],
P [auth E],
Q [auth E],
S [auth E],
U [auth F],
V [auth F],
Y [auth H],
Z [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
L [auth D],
X [auth F]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.168 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.714α = 90
b = 219.714β = 90
c = 82.964γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-09-07
    Changes: Database references, Derived calculations
  • Version 1.2: 2022-09-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description