9BW8 | pdb_00009bw8

Structure of P450Blt from Micromonospora sp. MW-13 in Complex with Fluorinated Biarylitide

PDB DOI: https://doi.org/10.2210/pdb9BW8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Micromonospora sp. MW-13, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-21 Released: 2024-11-20
Deposition Author(s): Hansen, M.H., Cryle, M.J., Zhao, Y.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.207 (Depositor), 0.206 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.180 (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

Loss of fluorine during crosslinking by the biarylitide P450 Blt proceeds due to restricted peptide orientation.

Zhao, Y., Gullick, J., Hansen, M.H., Coe, L., Treisman, M., Schittenhelm, R.B., McKay, A., Murray, L.A.M., Tailhades, J., De Voss, J.J., Krenske, E.H., Cryle, M.J.

(2024) Chem Commun (Camb) 60: 13951-13954

PubMed: 39512132 Search on PubMed
DOI: https://doi.org/10.1039/d4cc04092a
Primary Citation Related Structures:
9BW8

PubMed Abstract:
The biarylitide crosslinking enzyme P450 _Blt can perform crosslinking between m -F-Tyr-3 and His-5 residues within peptide substrates with concomitant and specific loss of fluorine. Our investigations suggest that a small intrinsic preference for coupling ipso to fluorine is magnified by the binding of the peptide in a specific orientation that enforces the loss of fluorine during peptide crosslinking, likely via a two-step reaction mechanism involving the non-enzyme catalysed reductive elimination of fluoride.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia. max.cryle@monash.edu.

Macromolecule Content

Total Structure Weight: 139.18 kDa
Atom Count: 9,403
Modeled Residue Count: 1,147
Deposited Residue Count: 1,265
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450-SU1	A, B, C	420	Micromonospora sp. MW-13	Mutation(s): 0 Gene Names: C5N14_21030 EC: 1.14
UniProt
Find proteins for A0ACD6BAH8 (Micromonospora sp. MW-13) Explore A0ACD6BAH8 Go to UniProtKB: A0ACD6BAH8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAH8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluorinated Biarylitide	D [auth E]	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain G [auth A]	G [auth A], K [auth B], M [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth C]
TFA Query on TFA Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], I [auth B], J [auth B], L [auth C]	trifluoroacetic acid C₂ H F₃ O₂ DTQVDTLACAAQTR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]