Skip to main content

 4Q7E | pdb_00004q7e

Non-phosphorylated HemR Receiver Domain from Leptospira biflexa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.185 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.140 (Depositor) 
  • R-Value Observed: 
    0.141 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4Q7E

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

Literature

HemR is an OmpR/PhoB-like response regulator from Leptospira, which simultaneously effects transcriptional activation and repression of key haem metabolism genes.

Morero, N.R., Botti, H., Nitta, K.R., Carrion, F., Obal, G., Picardeau, M., Buschiazzo, A.

(2014) Mol Microbiol 94: 340-352

  • DOI: https://doi.org/10.1111/mmi.12763
  • Primary Citation Related Structures: 
    4Q7E

  • PubMed Abstract: 

    Several Leptospira species cause leptospirosis, the most extended zoonosis worldwide. In bacteria, two-component systems constitute key signalling pathways, some of which are involved in pathogenesis. The physiological roles of two-component systems in Leptospira are largely unknown, despite identifying several dozens within their genomes. Biochemical confirmation of an operative phosphorelaying two-component system has been obtained so far only for the Hklep/Rrlep pair. It is known that hklep/rrlep knockout strains of Leptospira biflexa result in haem auxotrophy, although their de novo biosynthesis machinery remains fully functional. Haem is essential for Leptospira, but information about Hklep/Rrlep effector function(s) and target(s) is still lacking. We are now reporting a thorough molecular characterization of this system, which we rename HemK/HemR. The DNA HemR-binding motif was determined, and found within the genomes of saprophyte and pathogenic Leptospira. In this way, putative HemR-regulated genes were pinpointed, including haem catabolism-related (hmuO - haem oxygenase) and biosynthesis-related (the hemA/C/D/B/L/E/N/G operon). Specific HemR binding to these two promoters was quantified, and a dual function was observed in vivo, inversely repressing the hmuO, while activating the hemA operon transcription. The crystal structure of HemR receiver domain was determined, leading to a mechanistic model for its dual regulatory role.


  • Organizational Affiliation: 
    • Institut Pasteur de Montevideo, Unit of Protein Crystallography, 2020 Mataojo, 11400, Montevideo, Uruguay.

Macromolecule Content 

  • Total Structure Weight: 30.27 kDa 
  • Atom Count: 2,584 
  • Modeled Residue Count: 249 
  • Deposited Residue Count: 258 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Response regulator of a two component regulatory system
A, B
129Leptospira biflexa serovar Patoc strain 'Patoc 1 (Ames)Mutation(s): 0 
Gene Names: LBF_1368
UniProt
Find proteins for A5JUR5 (Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris))
Explore A5JUR5 
Go to UniProtKB:  A5JUR5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5JUR5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free:  0.185 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.140 (Depositor) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.446α = 90
b = 62.963β = 90
c = 66.977γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations