6A8A

Ribokinase from Leishmania donovani with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Unraveling structural insights of ribokinase from Leishmania donovani.

Gatreddi, S.Pillalamarri, V.Vasudevan, D.Addlagatta, A.Qureshi, I.A.

(2019) Int J Biol Macromol 136: 253-265

  • DOI: 10.1016/j.ijbiomac.2019.06.001
  • Primary Citation of Related Structures:  
    5ZWY, 6A8B, 6A8A, 6A8C

  • PubMed Abstract: 
  • Ribokinase (RK) is an ATP dependent sugar kinase that enables the entry of ribose in the metabolism. Leishmania accumulates ribose into the cytosol through hydrolysis of nucleosides and by transport from the extracellular environment. Activation by R ...

    Ribokinase (RK) is an ATP dependent sugar kinase that enables the entry of ribose in the metabolism. Leishmania accumulates ribose into the cytosol through hydrolysis of nucleosides and by transport from the extracellular environment. Activation by RK is critical to mobilize the ribose into the metabolism of Leishmania. To understand the catalytic role, the crystal structure of RK (LdRK) from L. donovani was determined in the apo and complex forms with several nucleotides (ATP, AMPPCP and ADP) in the presence of Na + ion. The dual insertion of five amino acid stretches makes LdRK structurally unique from other reported structures of RKs. The structure of LdRK-ATP provided the basis for positioning of γ-phosphate of ATP by conserved -GAGD- motif. Liganded and unliganded structures of LdRK exists in similar conformation, which suggests binding of nucleotides does not make any significant conformational changes in nucleotide-bound structures. Substitution of a conserved asparagine with phenylalanine in ribose binding pocket differentiates the LdRK from other RKs. Glycerol molecule bound in the substrate binding pocket mimics the enzyme-substrate interactions but in turn, hampers the binding of ribose to LdRK. Comparative structural analysis revealed the flexibility of γ-phosphate, which adopts multiple conformations in the absence of divalent metal ion and ribose. Similar to other RKs, LdRK is also dependent on monovalent as well as divalent cations for its catalytic activity.


    Organizational Affiliation

    Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India. Electronic address: insaf@uohyd.ac.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RibokinaseAB349Leishmania donovani BPK282A1Mutation(s): 0 
Gene Names: LDBPK_270430
EC: 2.7.1.15
Find proteins for E9BIX7 (Leishmania donovani (strain BPK282A1))
Explore E9BIX7 
Go to UniProtKB:  E9BIX7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.902α = 90
b = 99.902β = 90
c = 125.554γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references