8SM8 | pdb_00008sm8

Air-oxidized A. ca TruffO expressed from M9 minimal medium supplemented with Fe

PDB DOI: https://doi.org/10.2210/pdb8SM8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Afipia carboxidovorans OM5
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: 2.00 Å
R-Value Free:
0.252 (Depositor), 0.250 (DCC)
R-Value Work:
0.192 (Depositor), 0.193 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacs.3c12131
Primary Citation 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: 176.46 kDa
Atom Count: 11,818
Modeled Residue Count: 1,376
Deposited Residue Count: 1,552
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative amidohydrolase	A [auth G], B [auth A], C [auth D], D [auth J]	388	Afipia carboxidovorans OM5	Mutation(s): 0 Gene Names: OCA5_c12850
UniProt
Find proteins for B6JH23 (Afipia carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5)) Explore B6JH23 Go to UniProtKB: B6JH23
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B6JH23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G SDF format, chain J [auth A] SDF format, chain O [auth D] SDF format, chain R [auth J] MOL2 format, chain G MOL2 format, chain J [auth A] MOL2 format, chain O [auth D] MOL2 format, chain R [auth J] mmCIF format, chain G mmCIF format, chain J [auth A] mmCIF format, chain O [auth D] mmCIF format, chain R [auth J]	G, J [auth A], O [auth D], R [auth J]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G Focus chain J [auth A] Focus chain O [auth D] Focus chain R [auth J] Interactions & Density Focus chain G Focus chain J [auth A] Focus chain O [auth D] Focus chain R [auth J]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain E [auth G] SDF format, chain F [auth G] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain P [auth J] SDF format, chain Q [auth J] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth G] MOL2 format, chain F [auth G] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain P [auth J] MOL2 format, chain Q [auth J] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth G] mmCIF format, chain F [auth G] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain P [auth J] mmCIF format, chain Q [auth J] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	E [auth G] F [auth G] H [auth A] I [auth A] M [auth D] E [auth G], F [auth G], H [auth A], I [auth A], M [auth D], N [auth D], P [auth J], Q [auth J]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth G] Focus chain F [auth G] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth D] Focus chain N [auth D] Focus chain P [auth J] Focus chain Q [auth J] Interactions & Density Focus chain E [auth G] Focus chain F [auth G] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth D] Focus chain N [auth D] Focus chain P [auth J] Focus chain Q [auth J]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]