8SM7

Air-oxidized G. y4 TruffO expressed from M9 minimal medium supplemented with Fe

PDB DOI: https://doi.org/10.2210/pdb8SM7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paenibacillus sp. Y412MC10
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-04-25 Released: 2024-03-13
Deposition Author(s): Liu, C., Rittle, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.242
R-Value Work: 0.199
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Bioinformatic Discovery of a Cambialistic Monooxygenase.

Liu, C., Powell, M.M., Rao, G., Britt, R.D., Rittle, J.

(2024) J Am Chem Soc 146: 1783-1788

PubMed: 38198693 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jacs.3c12131
Primary Citation of Related Structures:
8SM6, 8SM7, 8SM8, 8SM9, 8SMA

PubMed Abstract:
Dinuclear monooxygenases mediate challenging C-H bond oxidation reactions throughout nature. Many of these enzymes are presumed to exclusively utilize diiron cofactors. Herein we report the bioinformatic discovery of an orphan dinuclear monooxygenase that preferentially utilizes a heterobimetallic manganese-iron (Mn/Fe) cofactor to mediate an O ₂-dependent C-H bond hydroxylation reaction. Unlike the structurally similar Mn/Fe-dependent monooxygenase AibH2, the diiron form of this enzyme (SfbO) exhibits a nascent enzymatic activity. This behavior raises the possibility that many other dinuclear monooxygenases may be endowed with the capacity to harness cofactors with a variable metal content.

Organizational Affiliation

Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.

Macromolecule Content

Total Structure Weight: 157.16 kDa
Atom Count: 11,355
Modelled Residue Count: 1,388
Deposited Residue Count: 1,404
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase 2	A, B, C [auth D], D [auth G]	351	Paenibacillus sp. Y412MC10	Mutation(s): 0 Gene Names: GYMC10_1268
UniProt
Find proteins for D3EI84 (Geobacillus sp. (strain Y412MC10)) Explore D3EI84 Go to UniProtKB: D3EI84
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3EI84
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth G] SDF format, chain M [auth G] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth G] MOL2 format, chain M [auth G]	E [auth A] F [auth A] G [auth B] H [auth B] J [auth D] E [auth A], F [auth A], G [auth B], H [auth B], J [auth D], K [auth D], L [auth G], M [auth G]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth G] Focus chain M [auth G] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth G] Focus chain M [auth G]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth G] SDF format, chain O [auth G] MOL2 format, chain I [auth B] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G]	I [auth B], N [auth G], O [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain N [auth G] Focus chain O [auth G] Interactions & Density Focus chain I [auth B] Focus chain N [auth G] Focus chain O [auth G]