5OI0

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) in complex with serine and glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structural characterization of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation.

Cereija, T.B.Alarico, S.Lourenco, E.C.Manso, J.A.Ventura, M.R.Empadinhas, N.Macedo-Ribeiro, S.Pereira, P.J.B.

(2019) Iucrj 6: 572-585

  • DOI: 10.1107/S2052252519005372
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacteria are challenged to adapt to environmental variations in order to survive. Under nutritional stress, several bacteria are able to slow down their metabolism into a nonreplicating state and wait for favourable conditions. It is almost universal ...

    Bacteria are challenged to adapt to environmental variations in order to survive. Under nutritional stress, several bacteria are able to slow down their metabolism into a nonreplicating state and wait for favourable conditions. It is almost universal that bacteria accumulate carbon stores to survive during this nonreplicating state and to fuel rapid proliferation when the growth-limiting stress disappears. Mycobacteria are exceedingly successful in their ability to become dormant under harsh circumstances and to be able to resume growth when conditions are favourable. Rapidly growing mycobacteria accumulate glucosylglycerate under nitrogen-limiting conditions and quickly mobilize it when nitrogen availability is restored. The depletion of intracellular glucosyl-glycerate levels in Mycolicibacterium hassiacum (basonym Mycobacterium hassiacum ) was associated with the up-regulation of the gene coding for glucosylglycerate hydrolase (GgH), an enzyme that is able to hydrolyse glucosylglycerate to glycerate and glucose, a source of readily available energy. Highly conserved among unrelated phyla, GgH is likely to be involved in bacterial reactivation following nitrogen starvation, which in addition to other factors driving mycobacterial recovery may also provide an opportunity for therapeutic intervention, especially in the serious infections caused by some emerging opportunistic pathogens of this group, such as Mycobacteroides abscessus (basonym Mycobacterium abscessus ). Using a combination of biochemical methods and hybrid structural approaches, the oligomeric organization of M. hassiacum GgH was determined and molecular determinants of its substrate binding and specificity were unveiled.


    Organizational Affiliation

    CNC - Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Coimbra, Portugal.,ITQB - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,IIIUC - Instituto de Investigação Interdisciplinar, Universidade de Coimbra, Coimbra, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, B
448Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)Mutation(s): 0 
Find proteins for K5BDL0 (Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849))
Go to UniProtKB:  K5BDL0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SER
Query on SER

Download SDF File 
Download CCD File 
A, B
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 85.981α = 90.00
b = 158.802β = 90.00
c = 87.827γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPOCI-01-0145-FEDER-007274
Norte Portugal Regional Operational Programme NORTE 2020PortugalNorte-01-0145-FEDER-000012

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-05-15
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2019-07-31
    Type: Data collection, Database references