8H58 | pdb_00008h58

Crystal structure of YhaJ effector binding domain

PDB DOI: https://doi.org/10.2210/pdb8H58/pdb

Classification: TRANSCRIPTION
Organism(s): Escherichia coli
Expression System: Escherichia coli DH5[alpha]
Mutation(s): No

Deposited: 2022-10-12 Released: 2023-10-25
Deposition Author(s): Kim, M., Ryu, S.E.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.236 (Depositor), 0.203 (DCC)
R-Value Work:
0.177 (Depositor), 0.157 (DCC)

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

Structural basis of transcription factor YhaJ for DNT detection.

Kim, M., Kang, R., Jeon, T.J., Ryu, S.E.

(2023) iScience 26: 107984-107984

PubMed: 37822509 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.isci.2023.107984
Primary Citation Related Structures:
8H58, 8H5A

PubMed Abstract:
Detection of landmines without harming personnel is a global issue. The bacterial transcription factor YhaJ selectively detects metabolites of explosives, and it can be used as a key component of DNT biosensors. However, the wild-type YhaJ has a binding affinity that is not sufficient for the detection of trace amounts of explosives leaked from landmines buried in the soil. Here, we report crystal structures of the effector-binding domain of YhaJ in both the apo- and effector-bound forms. A structural comparison of the two forms revealed that the loop above the primary effector-binding site significantly switches its conformation upon effector binding. The primary effector-binding site involves hydrophobic and polar interactions, having specificity to hydroxyl-substituted benzene compounds. The structures explain the mechanism of activity-enhancing mutations and provide information for the rational engineering of YhaJ biosensors for the sensitive detection of explosives.

Organizational Affiliation

Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04673, Republic of Korea.

Macromolecule Content

Total Structure Weight: 370.32 kDa
Atom Count: 25,530
Modeled Residue Count: 3,245
Deposited Residue Count: 3,312
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator YhaJ	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	207	Escherichia coli	Mutation(s): 0 Gene Names: yhaJ
UniProt
Find proteins for P67660 (Escherichia coli (strain K12)) Explore P67660 Go to UniProtKB: P67660
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P67660
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain BA [auth M] SDF format, chain CA [auth N] SDF format, chain DA [auth O] SDF format, chain EA [auth P] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain U [auth F] SDF format, chain V [auth G] SDF format, chain W [auth H] SDF format, chain X [auth I] SDF format, chain Y [auth J] SDF format, chain Z [auth L] MOL2 format, chain AA [auth L] MOL2 format, chain BA [auth M] MOL2 format, chain CA [auth N] MOL2 format, chain DA [auth O] MOL2 format, chain EA [auth P] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth F] MOL2 format, chain V [auth G] MOL2 format, chain W [auth H] MOL2 format, chain X [auth I] MOL2 format, chain Y [auth J] MOL2 format, chain Z [auth L] mmCIF format, chain AA [auth L] mmCIF format, chain BA [auth M] mmCIF format, chain CA [auth N] mmCIF format, chain DA [auth O] mmCIF format, chain EA [auth P] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth F] mmCIF format, chain V [auth G] mmCIF format, chain W [auth H] mmCIF format, chain X [auth I] mmCIF format, chain Y [auth J] mmCIF format, chain Z [auth L]	AA [auth L] BA [auth M] CA [auth N] DA [auth O] EA [auth P] AA [auth L], BA [auth M], CA [auth N], DA [auth O], EA [auth P], Q [auth A], R [auth A], S [auth C], T [auth D], U [auth F], V [auth G], W [auth H], X [auth I], Y [auth J], Z [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth L] Focus chain BA [auth M] Focus chain CA [auth N] Focus chain DA [auth O] Focus chain EA [auth P] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth L] Focus chain BA [auth M] Focus chain CA [auth N] Focus chain DA [auth O] Focus chain EA [auth P] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth L]