4U94

Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway.

Fraga, J.Maranha, A.Mendes, V.Pereira, P.J.Empadinhas, N.Macedo-Ribeiro, S.

(2015) Sci Rep 5: 8026-8026

  • DOI: https://doi.org/10.1038/srep08026
  • Primary Citation of Related Structures:  
    4U94, 4U98, 4WZY

  • PubMed Abstract: 

    A novel four-step pathway identified recently in mycobacteria channels trehalose to glycogen synthesis and is also likely involved in the biosynthesis of two other crucial polymers: intracellular methylglucose lipopolysaccharides and exposed capsular glucan. The structures of three of the intervening enzymes - GlgB, GlgE, and TreS - were recently reported, providing the first templates for rational drug design. Here we describe the structural characterization of the fourth enzyme of the pathway, mycobacterial maltokinase (Mak), uncovering a eukaryotic-like kinase (ELK) fold, similar to methylthioribose kinases and aminoglycoside phosphotransferases. The 1.15 Å structure of Mak in complex with a non-hydrolysable ATP analog reveals subtle structural rearrangements upon nucleotide binding in the cleft between the N- and the C-terminal lobes. Remarkably, this new family of ELKs has a novel N-terminal domain topologically resembling the cystatin family of protease inhibitors. By interfacing with and restraining the mobility of the phosphate-binding region of the N-terminal lobe, Mak's unusual N-terminal domain might regulate its phosphotransfer activity and represents the most likely anchoring point for TreS, the upstream enzyme in the pathway. By completing the gallery of atomic-detail models of an essential pathway, this structure opens new avenues for the rational design of alternative anti-tubercular compounds.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltokinase454Mycolicibacterium vanbaalenii PYR-1Mutation(s): 0 
Gene Names: makMvan_5735
EC: 2.7.1.175
UniProt
Find proteins for A1TH50 (Mycolicibacterium vanbaalenii (strain DSM 7251 / JCM 13017 / BCRC 16820 / KCTC 9966 / NRRL B-24157 / PYR-1))
Explore A1TH50 
Go to UniProtKB:  A1TH50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1TH50
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.947α = 90
b = 73.409β = 90
c = 106.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SHELXDEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FCTPortugalFCOMP-01-0124-FEDER-028359
FCTPortugalFCOMP-01-0124-FEDER-014321
FCTPortugalFCOMP-01-0124-FEDER-014187
ON.2 - O Novo NortePortugalNORTE-07-0124-000002 - Host-Pathogen Interactions

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release