GlnH bound to Asn, Mycobacterium tuberculosis

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


An Aspartate-Specific Solute-Binding Protein Regulates Protein Kinase G Activity To Control Glutamate Metabolism in Mycobacteria.

Bhattacharyya, N.Nkumama, I.N.Newland-Smith, Z.Lin, L.Y.Yin, W.Cullen, R.E.Griffiths, J.S.Jarvis, A.R.Price, M.J.Chong, P.Y.Wallis, R.O'Hare, H.M.

(2018) mBio 9

  • DOI: https://doi.org/10.1128/mBio.00931-18
  • Primary Citation of Related Structures:  
    6H1U, 6H20, 6H2T

  • PubMed Abstract: 

    Signaling by serine/threonine phosphorylation controls diverse processes in bacteria, and identification of the stimuli that activate protein kinases is an outstanding question in the field. Recently, we showed that nutrients stimulate phosphorylation of the protein kinase G substrate GarA in Mycobacterium smegmatis and Mycobacterium tuberculosis and that the action of GarA in regulating central metabolism depends upon whether it is phosphorylated. Here we present an investigation into the mechanism by which nutrients activate PknG. Two unknown genes were identified as co-conserved and co-expressed with PknG: their products were a putative lipoprotein, GlnH, and putative transmembrane protein, GlnX. Using a genetic approach, we showed that the membrane protein GlnX is functionally linked to PknG. Furthermore, we determined that the ligand specificity of GlnH matches the amino acids that stimulate GarA phosphorylation. We determined the structure of GlnH in complex with different amino acid ligands (aspartate, glutamate, and asparagine), revealing the structural basis of ligand specificity. We propose that the amino acid concentration in the periplasm is sensed by GlnH and that protein-protein interaction allows transmission of this information across the membrane via GlnX to activate PknG. This sensory system would allow regulation of nutrient utilization in response to changes in nutrient availability. The sensor, signaling, and effector proteins are conserved throughout the Actinobacteria , including the important human pathogen Mycobacterium tuberculosis , industrial amino acid producer Corynebacterium glutamicum , and antibiotic-producing Streptomyces species. IMPORTANCE Tuberculosis (TB) kills 5,000 people every day, and the prevalence of multidrug-resistant TB is increasing in every country. The processes by which the pathogen Mycobacterium tuberculosis senses and responds to changes in its environment are attractive targets for drug development. Bacterial metabolism differs dramatically between growing and dormant cells, and these changes are known to be important in pathogenesis of TB. Here, we used genetic and biochemical approaches to identify proteins that allow M. tuberculosis to detect amino acids in its surroundings so that it can regulate its metabolism. We have also shown how individual amino acids are recognized. The findings have broader significance for other actinobacterial pathogens, such as nontuberculous mycobacteria, as well as Actinobacteria used to produce billions of dollars of amino acids and antibiotics every year.

  • Organizational Affiliation

    Leicester Tuberculosis Research Group, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable glutamine-binding lipoprotein GlnH (GLNBP)287Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: glnHRv0411c
Find proteins for P96257 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P96257 
Go to UniProtKB:  P96257
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96257
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ASN

Download Ideal Coordinates CCD File 
C4 H8 N2 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.328α = 90
b = 81.298β = 90
c = 88.509γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_PC_16051

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description