8H8H | pdb_00008h8h

Crystal structure of the N-terminal domain of H-NS family protein TurB (TurB_nt50)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8H8H

This is version 1.2 of the entry. See complete history

Literature

Structural characterization of the native oligomerization mode of MvaT proteins in Pseudomonas.

Vasileva, D.Suzuki-Minakuchi, C.Arakawa, T.Moriwaki, Y.Yonezawa, K.Shimizu, N.Fujimoto, Z.Terada, T.Okada, K.Nojiri, H.

(2026) Microbiol Spectr : e0023526-e0023526

  • DOI: https://doi.org/10.1128/spectrum.00235-26
  • Primary Citation Related Structures: 
    8H8H

  • PubMed Abstract: 

    Histone-like protein H1 (H-NS) proteins are key regulators of horizontally acquired genes in enterobacteria. Functional analogs of H-NS, collectively known as H-NS family proteins, have been discovered in diverse bacteria and on large transmissible plasmids. These proteins share the ability to form oligomers through their N-terminal oligomerization domain, a feature critical for their regulatory functions. The N-terminal domain of MvaT proteins, members of the H-NS family proteins in pseudomonads, consists of a central and a terminal dimerization site. We previously elucidated the structure of the central dimerization site of TurB, an MvaT homolog in P. putida KT2440. Here, we solved the crystal and solution structures of its terminal dimerization site and generated a structural model of TurB in an oligomerized form. Our data show that the terminal dimerization site of TurB is composed of two helices connected by a flexible hinge. The results also reveal differences between the oligomerization manner of MvaT proteins and H-NS in enterobacteria. Residues forming salt bridges and hydrophobic interactions that stabilize the terminal dimerization site are relatively conserved among MvaT proteins encoded on the chromosomes of various Pseudomonas strains and plasmids. Previous studies have shown that Pseudomonas strains typically harbor plasmids encoding MvaT proteins, while enterobacteria carry plasmids encoding H-NS. Our results suggest that differences in the oligomerization domain of H-NS family proteins may be critical for the cross-talk between plasmids and the host chromosome.IMPORTANCEHorizontal gene transfer is a major driver of microbial evolution. H-NS family proteins are key factors in optimizing the transcription of newly acquired genes in host cells. Despite high sequence diversity among bacteria, these proteins share the ability to form oligomers along DNA, a critical property for their function. H-NS family proteins encoded both on large transmissible plasmids and on the chromosomes of host cells play an important role in the successful integration of new genetic sequences into the regulatory networks of microbes. Bacterial hosts typically harbor plasmids encoding the same type of H-NS family proteins as found on their chromosomes. Here, we characterized the structural basis for oligomerization of MvaT proteins, members of the H-NS family proteins in pseudomonads. Our findings reveal differences between the oligomerization mode of MvaT proteins and H-NS in enterobacteria, suggesting that these differences might impact the transmission routes of plasmids within microbial communities.


  • Organizational Affiliation
    • Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 54.72 kDa 
  • Atom Count: 3,255 
  • Modeled Residue Count: 404 
  • Deposited Residue Count: 464 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H-NS family protein MvaT
A, B, C, D, E
A, B, C, D, E, F, G, H
58Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: PP_3765
UniProt
Find proteins for Q88GF9 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88GF9 
Go to UniProtKB:  Q88GF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88GF9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.692α = 90
b = 63.303β = 90
c = 275.872γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K05408
Japan Society for the Promotion of Science (JSPS)Japan21H02097
Japan Science and TechnologyJapanJPMJER1502

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection
  • Version 1.2: 2026-04-22
    Changes: Database references, Structure summary