9OQT | pdb_00009oqt

N-hydroxylamine dehydratase (NohD) T98A/K167A mutant crystal structure with heme and N-hydroxylated ornithine (2.5h soak)

PDB DOI: https://doi.org/10.2210/pdb9OQT/pdb

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

Deposited: 2025-05-21 Released: 2025-12-03
Deposition Author(s): Higgins, M.A., Shi, X., Hoffarth, E.R., Du, Y.L., Ryan, K.S.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.214 (Depositor), 0.211 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)
R-Value Observed:
0.192 (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

Conversion of a Heme-Dependent Dehydratase to a Piperazate Synthase Reveals the Role of the Heme Propionate Group in N-N Bond-Formation.

Higgins, M.A., Mirotadze, N., Shi, X., Hoffarth, E.R., Du, Y.L., Ryan, K.S.

(2025) J Am Chem Soc 147: 39160-39168

PubMed: 41101755 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacs.5c08886
Primary Citation Related Structures:
9OQS, 9OQT, 9OQU, 9OQV, 9OQW, 9OQX, 9OQZ, 9OR0, 9OR1

PubMed Abstract:
Enzymes that form nitrogen-nitrogen bonds are employed in natural product biosynthesis and the nitrogen cycle. Piperazate synthase forms the cyclic hydrazine l-piperazic acid from l- N ⁵-OH-ornithine, using heme as a cofactor. In this work, we discover sequence-related enzyme NohD that instead reacts with l- N ⁵-OH-ornithine to release ammonia, and we solve its structure to 1.4 Å resolution. We then employ structure-guided site-directed mutagenesis to endow variants of NohD with piperazate synthase activity. Crystal structures of the NohD variants reveal how the heme propionate changes conformation, positioning it upward toward the amino nitrogen, where it is likely to activate the amine for N-N bond-formation. This study highlights a key structural requirement for N-N bond-formation and sets the stage for the development of new N-N-bond-forming catalysts.

Organizational Affiliation

Department of Chemistry, The University of British Columbia, Vancouver V6T 1Z1, Canada.

Macromolecule Content

Total Structure Weight: 46.74 kDa
Atom Count: 3,545
Modeled Residue Count: 408
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-hydroxylamine dehydratase (NohD)	A, B	206	Actinomadura luzonensis	Mutation(s): 0
UniProt
Find proteins for A0ABT0G6E0 (Actinomadura luzonensis) Explore A0ABT0G6E0 Go to UniProtKB: A0ABT0G6E0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABT0G6E0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
ONH (Subject of Investigation/LOI) Query on ONH Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	N~5~-hydroxy-L-ornithine C₅ H₁₂ N₂ O₃ OZMJDTPATROLQC-BYPYZUCNSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] H [auth B] I [auth B] C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]