7Q06 | pdb_00007q06

Crystal structure of TPADO in complex with 2-OH-TPA

PDB DOI: https://doi.org/10.2210/pdb7Q06/pdb

Classification: OXIDOREDUCTASE
Organism(s): Comamonas sp., Gallus gallus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-14 Released: 2022-03-30
Deposition Author(s): Zahn, M., Kincannon, W.M., DuBois, J.L., McGeehan, J.E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.202 (Depositor), 0.201 (DCC)
R-Value Work:
0.165 (Depositor), 0.163 (DCC)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 35312352 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2121426119
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 212.34 kDa
Atom Count: 14,895
Modeled Residue Count: 1,764
Deposited Residue Count: 1,875
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1	A, B, C	154	Comamonas 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3C1E2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2	D, E, F	428	Comamonas 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3C1D5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	G [auth H]	129	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8IB (Subject of Investigation/LOI) Query on 8IB Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain P [auth E] SDF format, chain T [auth F] MOL2 format, chain L [auth D] MOL2 format, chain P [auth E] MOL2 format, chain T [auth F] mmCIF format, chain L [auth D] mmCIF format, chain P [auth E] mmCIF format, chain T [auth F]	L [auth D], P [auth E], T [auth F]	2-Hydroxyterephthalic acid C₈ H₆ O₅ CDOWNLMZVKJRSC-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Focus chain P [auth E] Focus chain T [auth F] Interactions & Density Focus chain L [auth D] Focus chain P [auth E] Focus chain T [auth F]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain Q [auth F] SDF format, chain M [auth E] MOL2 format, chain I [auth D] MOL2 format, chain Q [auth F] MOL2 format, chain M [auth E] mmCIF format, chain I [auth D] mmCIF format, chain Q [auth F] mmCIF format, chain M [auth E]	I [auth D], M [auth E], Q [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain M [auth E] Focus chain Q [auth F] Interactions & Density Focus chain I [auth D] Focus chain M [auth E] Focus chain Q [auth F]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth D] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain R [auth F] SDF format, chain U [auth H] MOL2 format, chain H [auth B] MOL2 format, chain J [auth D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain R [auth F] MOL2 format, chain U [auth H] mmCIF format, chain H [auth B] mmCIF format, chain J [auth D] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E] mmCIF format, chain R [auth F] mmCIF format, chain U [auth H]	H [auth B] J [auth D] N [auth E] O [auth E] R [auth F] H [auth B], J [auth D], N [auth E], O [auth E], R [auth F], U [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Focus chain J [auth D] Focus chain N [auth E] Focus chain O [auth E] Focus chain R [auth F] Focus chain U [auth H] Interactions & Density Focus chain H [auth B] Focus chain J [auth D] Focus chain N [auth E] Focus chain O [auth E] Focus chain R [auth F] Focus chain U [auth H]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain S [auth F] MOL2 format, chain K [auth D] MOL2 format, chain S [auth F] mmCIF format, chain K [auth D] mmCIF format, chain S [auth F]	K [auth D], S [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Focus chain S [auth F] Interactions & Density Focus chain K [auth D] Focus chain S [auth F]