Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.28 kDa 
• Atom Count: 4053 
• Modelled Residue Count: 451 
• Deposited Residue Count: 454 
• Unique protein chains: 1

4WZY

Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway (ATP complex)

• PDB DOI: 10.2210/pdb4WZY/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium vanbaalenii PYR-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-20 Released: 2015-02-11 
• Deposition Author(s): Fraga, J., Empadinhas, N., Pereira, P.J.B., Macedo-Ribeiro, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

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

• PubMed: 25619172 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltokinase	A	454	Mycolicibacterium vanbaalenii PYR-1	Mutation(s): 0  Gene Names: mak, Mvan_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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.991	α = 90
b = 73.767	β = 90
c = 107.426	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-11-20 
• Released Date: 2015-02-11 
Deposition Author(s): Fraga, J., Empadinhas, N., Pereira, P.J.B., Macedo-Ribeiro, S.

Revision History  

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