9F1Q | pdb_00009f1q

Crystal structure of a DyP-type peroxidase Fireprot variant from Pseudomonas putida

PDB DOI: https://doi.org/10.2210/pdb9F1Q/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-04-19 Released: 2025-04-30
Deposition Author(s): Lorena, C., Borges, P.T., Frazao, C., Martins, L.O.
Funding Organization(s): Foundation for Science and Technology (FCT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.246 (Depositor), 0.247 (DCC)
R-Value Work:
0.219 (Depositor), 0.219 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Network Dynamics as Fingerprints of Thermostability in an In Silico-Engineered DyP-Type Peroxidase.

Rodrigues, C.F., Silva, D., Lorena, C., Borges, P.T., Masgrau, L., Martins, L.O.

(2025) ACS Catal 15: 15395-15409

PubMed: 40933351 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acscatal.5c03333
Primary Citation of Related Structures:
9F1O, 9F1Q

PubMed Abstract:
Stabilizing industrial enzymes is crucial for advancing environmentally responsible bioprocesses; however, the structural basis of thermostability remains incompletely understood. Here, we engineered thermostable variants of a tetrameric dye-decolorizing peroxidase (DyP) using two independent open-source design algorithms, yielding enzymes with significantly improved thermal performance and prolonged activity at elevated temperatures. Subsequent recombination strategies minimize the mutational burden while maintaining or enhancing stability. Structural and dynamic analyses of the thermostable variants revealed convergent features, including increased compactness, rigidity, and an enriched network of hydrogen bonds and hydrophobic interactions. Despite differing mutation profiles, stabilizing substitutions clustered in similar structural regions. Notably, the integration of dynamic modeling with protein correlation network analysis uncovered a previously unrecognized fingerprint of stabilization: highly connected structural networks characterized by denser and more persistent intra- and intermonomer interactions, greater internal cohesion, and enhanced cooperative dynamics. Tetramers exhibit long-range communication pathways and redundant routes, supporting coordinated motions that can hinder local unfolding and tetramer dissociation. These findings identify dynamic interaction networks as hypothetical new indicators of protein stability and offer a previously unexplored framework for rational enzyme design.

Organizational Affiliation

Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal.

Macromolecule Content

Total Structure Weight: 129.27 kDa
Atom Count: 9,495
Modeled Residue Count: 1,141
Deposited Residue Count: 1,144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dyp-type peroxidase family protein	A, B, C, D	286	Pseudomonas putida	Mutation(s): 21 Gene Names: PP_3248
UniProt
Find proteins for Q88HV5 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88HV5 Go to UniProtKB: Q88HV5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q88HV5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	G [auth A], J [auth B], N [auth C], R [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	E [auth A] F [auth A] H [auth A] I [auth B] L [auth B] E [auth A], F [auth A], H [auth A], I [auth B], L [auth B], M [auth C], Q [auth C], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain Q [auth C] Focus chain T [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	K [auth B], O [auth C], P [auth C], S [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D]