Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D182A variant in complex with glucosylglycerate

Experimental Data Snapshot

  • Resolution: 1.71 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

Starting Model: experimental
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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: https://doi.org/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. 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

    IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
448Mycolicibacterium hassiacum DSM 44199Mutation(s): 1 
Gene Names: C731_0006
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9WN (Subject of Investigation/LOI)
Query on 9WN

Download Ideal Coordinates CCD File 
L [auth A],
R [auth B]
(2R)-2-(alpha-D-glucopyranosyloxy)-3-hydroxypropanoic acid
C9 H16 O9
Query on PGE

Download Ideal Coordinates CCD File 
C6 H14 O4
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.292α = 90
b = 159.606β = 90
c = 91.043γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

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: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-15
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2019-07-31
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary