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 
  • R-Value Observed: 0.147 

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:  
    5OHC, 5OHZ, 5OI0, 5OI1, 5OIE, 5OIV, 5OIW, 5OJ4, 5OJU, 5OJV, 5ONT, 5ONZ, 5OO2, 6Q5T

  • 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 that bacteria accumulate carbon stores to survive during this nonreplicating state and to fuel rapid proliferation when the growth-limiting stress disappears ...

    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: 

    Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA, B448Mycolicibacterium hassiacum DSM 44199Mutation(s): 0 
Gene Names: C731_0006, ggh
EC: 3.2.1.208
UniProt
Find proteins for K5BDL0 (Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849))
Explore K5BDL0 
Go to UniProtKB:  K5BDL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK5BDL0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/467 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.981α = 90
b = 158.802β = 90
c = 87.827γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

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  (Full details and data files)

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