9FFJ | pdb_00009ffj

Artificial metalloenzyme with a nickel-based 1,10-phenanthroline cofactor and streptavidin N49M-S112V mutant

PDB DOI: https://doi.org/10.2210/pdb9FFJ/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-05-23 Released: 2025-01-15
Deposition Author(s): Lau, K., Wang, W., Pojer, F., Larabi, A.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free:
0.197 (Depositor), 0.193 (DCC)
R-Value Work:
0.177 (Depositor), 0.172 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Artificial Metalloenzymes with Two Catalytic Cofactors for Tandem Abiotic Transformations.

Wang, W., Tachibana, R., Zhang, K., Lau, K., Pojer, F., Ward, T.R., Hu, X.

(2025) Angew Chem Int Ed Engl 64: e202422783-e202422783

PubMed: 39760306 Search on PubMed
DOI: https://doi.org/10.1002/anie.202422783
Primary Citation of Related Structures:
9FFJ, 9FNR, 9FOA

PubMed Abstract:
Artificial metalloenzymes (ArMs) enable the integration of abiotic cofactors within a native protein scaffold, allowing for non-natural catalytic activities. Previous ArMs, however, have primarily relied on single cofactor systems, limiting them to only one catalytic function. Here we present an approach to construct ArMs embedding two catalytic cofactors based on the biotin-streptavidin technology. By incorporating multiple catalytic cofactors into the four binding sites of streptavidin, we engineered programmable ArMs for tandem abiotic transformations including an enantioselective formal C-H hydroxylation and a photooxidation-Michael addition. This work thus outlines a promising strategy for the development of ArMs embedding multiple cofactors.

Organizational Affiliation

EPFL: Ecole Polytechnique Federale de Lausanne, chemistry, SWITZERLAND.

Macromolecule Content

Total Structure Weight: 17.72 kDa
Atom Count: 1,136
Modelled Residue Count: 121
Deposited Residue Count: 159
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	159	Streptomyces avidinii	Mutation(s): 2
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ICD (Subject of Investigation/LOI) Query on A1ICD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-methyl-N-[(4,4,6,6-tetrahydroxy-4,6-dioxido-1,3,3a,5,6a-tetrahydrothien[3,4-d]imidazol-4-ium-2-yl)methyl]-5-(2,4,4-trihydroxy-2-keto-3,3a,5,6-tetrahydro-1H-thien[3,4-d]imidazol-4-ium-6-yl C₂₄ H₂₉ N₅ Ni O₆ S FBTOJTGKJUIUQP-ZJHXQHFDSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain F [auth A] MOL2 format, chain B [auth A] MOL2 format, chain F [auth A] mmCIF format, chain B [auth A] mmCIF format, chain F [auth A]	B [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain F [auth A]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]