8PC7 | pdb_00008pc7

STRUCTURE OF ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY) COMPLEXED WITH A DERIVATIVE OF BIPYRIDINE PHOSPHONATE

PDB DOI: https://doi.org/10.2210/pdb8PC7/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli MC1061
Mutation(s): No

Deposited: 2023-06-09 Released: 2023-07-19
Deposition Author(s): Cea-Rama, I., Sanz-Aparicio, J.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.253 (Depositor), 0.290 (DCC)
R-Value Work:
0.244 (Depositor)
R-Value Observed:
0.244 (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

Transforming an esterase into an enantioselective catecholase through bioconjugation of a versatile metal-chelating inhibitor.

Fernandez-Lopez, L., Cea-Rama, I., Alvarez-Malmagro, J., Ressmann, A.K., Gonzalez-Alfonso, J.L., Coscolin, C., Shahgaldian, P., Plou, F.J., Modregger, J., Pita, M., Sanz-Aparicio, J., Ferrer, M.

(2023) Chem Commun (Camb) 59: 9469-9472

PubMed: 37376994 Search on PubMed
DOI: https://doi.org/10.1039/d3cc01946b
Primary Citation Related Structures:
8PC7

PubMed Abstract:
Metal complexes introduced into protein scaffolds can generate versatile biomimetic catalysts endowed with a variety of catalytic properties. Here, we synthesized and covalently bound a bipyridinyl derivative to the active centre of an esterase to generate a biomimetic catalyst that shows catecholase activity and enantioselective catalytic oxidation of (+)-catechin.

Organizational Affiliation

Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain. mferrer@icp.csic.es.

Macromolecule Content

Total Structure Weight: 162.81 kDa
Atom Count: 10,427
Modeled Residue Count: 1,343
Deposited Residue Count: 1,472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B, C, D	368	metagenome	Mutation(s): 0
UniProt
Find proteins for A0ACD6B906 (uncultured bacterium) Explore A0ACD6B906 Go to UniProtKB: A0ACD6B906
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B906
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZK8 (Subject of Investigation/LOI) Query on ZK8 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	F [auth A], H [auth B], L [auth C], N [auth D]	hexyl-[2-(3-oxidanylpyridin-2-yl)pyridin-3-yl]oxy-phosphinic acid C₁₆ H₂₁ N₂ O₄ P QYCWYIQRYAMGGW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C]	J [auth C], K [auth C], M [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.253 (Depositor), 0.290 (DCC)
R-Value Work: 0.244 (Depositor)
R-Value Observed: 0.244 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.755	α = 90
b = 189.39	β = 111.93
c = 75.954	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-19

Deposition Author(s):

Cea-Rama, I.

Sanz-Aparicio, J.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	Project BIO2016-76601-C3-3-R
Spanish Ministry of Economy and Competitiveness	Spain	Project PID2019-105838RB-C33