9YPI | pdb_00009ypi

MboA HDO apo structure

PDB DOI: https://doi.org/10.2210/pdb9YPI/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Pseudomonas syringae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-14 Released: 2026-05-06
Deposition Author(s): Badding, E.D., Kissman, E.N., Chang, M.C.Y.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.221 (Depositor), 0.223 (DCC)
R-Value Work:
0.187 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Discovery of a Structurally Distinct Acetylenase in the Biosynthesis of Mangotoxin.

Badding, E.D., Kissman, E.N., Velculescu, S.V., Chang, M.C.Y.

(2026) J Am Chem Soc 148: 18724-18732

PubMed: 42048656 Search on PubMed
DOI: https://doi.org/10.1021/jacs.5c21680
Primary Citation Related Structures:
9YPI, 9YPL, 9YPM

PubMed Abstract:
Amino acids, peptides, and proteins play pivotal roles in medicine, materials, and catalysis, with their functions largely dictated by their side-chain functionality. Recent studies have shown that heme oxygenase-like domain-containing oxidases (HDOs) catalyze a broad range of interesting chemical reactions on amino acids and their derivatives to produce structurally diverse target structures. Using a bioinformatics approach, the mangotoxin biosynthetic operon was found to house an unannotated HDO, MboA, along with a dedicated redox partner, MboB. We show that MboA catalyzes alkyne formation by iterative desaturations on the side-chain of a peptide substrate, where the transformation between alkene and alkyne is gated by MboB. The crystal structure of Fe(II) ₂-MboA reveals an unexpectedly short Fe-Fe distance, suggesting that the activation of strong C(sp ²)-H bonds may utilize a mechanism distinct from other HDOs and expands the scope of known HDO chemistry.

Organizational Affiliation

Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.

Macromolecule Content

Total Structure Weight: 115.06 kDa
Atom Count: 7,906
Modeled Residue Count: 926
Deposited Residue Count: 1,000
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mangotoxin biosynthesis protein MboA	A, B, C, D	250	Pseudomonas syringae	Mutation(s): 0 Gene Names: BW686_01200
UniProt
Find proteins for A0A244EXR3 (Pseudomonas syringae) Explore A0A244EXR3 Go to UniProtKB: A0A244EXR3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A244EXR3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain J [auth A] SDF format, chain U [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B]	DA [auth D], EA [auth D], J [auth A], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain J [auth A] Focus chain U [auth B] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain J [auth A] Focus chain U [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain W [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain W [auth B]	M [auth A], N [auth A], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain W [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain W [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] CA [auth D] E [auth A] F [auth A] AA [auth C], BA [auth C], CA [auth D], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], X [auth C], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain V [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain V [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain V [auth B]	K [auth A], L [auth A], V [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain V [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain V [auth B]