9W4V | pdb_00009w4v

Structure of transcription factor in complex with D-allo-Ile

PDB DOI: https://doi.org/10.2210/pdb9W4V/pdb

Classification: TRANSCRIPTION
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-01 Released: 2026-03-25
Deposition Author(s): Sakuraba, H., Ohshima, T., Yoneda, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.271 (Depositor), 0.269 (DCC)
R-Value Work:
0.208 (Depositor), 0.216 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: in silico
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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

A distinct gene expression mechanism for d-amino acid utilization in hyperthermophilic archaeon Pyrococcus horikoshii.

Kawakami, R., Kawase, T., Uehara, T., Sakuraba, H., Matsuzawa, T., Hayashi, J., Ohshima, T.

(2026) FEBS J

PubMed: 41991193 Search on PubMed
DOI: https://doi.org/10.1111/febs.70545
Primary Citation Related Structures:
9W4V, 9W4W

PubMed Abstract:
Growing the hyperthermophilic archaeon Pyrococcus horikoshii OT-3 in medium supplemented with d-allo-Ile instead of l-Ile markedly upregulates the activity of broad substrate specificity amino acid racemase (BAR). In P. horikoshii genome, the BAR gene (PH0138) forms a cluster with PH0137, which encodes a putative transporter protein, and PH0140 that encodes a feast/famine regulatory protein (FFRP), involved in the transcriptional regulation of metabolic pathway genes. Here, we performed gene expression, protein-DNA interaction, and crystallographic analyses to elucidate the expression mechanism of the BAR cluster. Gene expression analysis revealed that d-allo-Ile simultaneously induces PH0138 and PH0137. Electrophoretic mobility shift assays demonstrated that the PH0140 protein binds to the PH0137 promoter in the presence of l-Ile, but this interaction is disrupted by d-allo-Ile, identifying PH0140 as a d-amino acid-responsive regulatory protein (DARP). The crystal structures of DARP bound to l-Ile and d-allo-Ile were compared with those of another FFRP family member, P. horikoshii FL11. Our findings reveal a dimeric arrangement of l-Ile-bound DARP resembling the DNA-bound (open) form of FL11, whereas d-allo-Ile-bound DARP corresponds to the DNA-unbound (closed) form. These conformational changes result from subtle alterations in hydrogen bonding around the coregulators. Furthermore, cultivation in d-allo-Ile substitution medium only impacted the expression of PH0138 and PH0137, and not the other genes, suggesting that DARP regulates a more limited gene set than FL11. Cumulatively, these results reveal a distinct mechanism by which an FFRP homolog controls d-amino acid utilization.

Organizational Affiliation

Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Japan.

Macromolecule Content

Total Structure Weight: 40.83 kDa
Atom Count: 2,437
Modeled Residue Count: 294
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized HTH-type transcriptional regulator PH0140	A, B	178	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: PH0140
UniProt
Find proteins for O57880 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57880 Go to UniProtKB: O57880
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O57880
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
28J (Subject of Investigation/LOI) Query on 28J Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	D-alloisoleucine C₆ H₁₃ N O₂ AGPKZVBTJJNPAG-CRCLSJGQSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]