6K91

Pyridoxal Kinase from Leishmania donovani in complex with ADP and Pyridoxine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


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Literature

Structural attributes and substrate specificity of pyridoxal kinase from Leishmania donovani.

Are, S.Gatreddi, S.Jakkula, P.Qureshi, I.A.

(2020) Int.J.Biol.Macromol. 152: 812-827

  • DOI: 10.1016/j.ijbiomac.2020.02.257
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzyme pyridoxal kinase (PdxK) catalyzes the conversion of pyridoxal to pyridoxal-5'-phosphate (PLP) using ATP as the co-factor. The product pyridoxal-5'-phosphate plays a key role in several biological processes such as transamination, decarboxy ...

    The enzyme pyridoxal kinase (PdxK) catalyzes the conversion of pyridoxal to pyridoxal-5'-phosphate (PLP) using ATP as the co-factor. The product pyridoxal-5'-phosphate plays a key role in several biological processes such as transamination, decarboxylation and deamination. In the present study, full-length ORF of PdxK from Leishmania donovani (LdPdxK) was cloned and then purified using affinity chromatography. LdPdxK exists as a homo-dimer in solution and shows more activity at near to physiological pH. Biochemical analysis of LdPdxK with pyridoxal, pyridoxamine, pyridoxine and ginkgotoxin revealed its affinity preference towards different substrates. The secondary structure analysis using circular dichroism spectroscopy showed LdPdxK to be predominantly α-helical in organization which tends to decline at lower and higher pH. Simultaneously, LdPdxK was crystallized and its three-dimensional structure in complex with ADP and different substrates were determined. Crystal structure of LdPdxK delineated that it has a central core of β-sheets surrounded by α-helices with a conserved GTGD ribokinase motif. The structures of LdPdxK disclosed no major structural changes between ADP and ADP- substrate bound structures. In addition, comparative structural analysis highlighted the key differences between the active site pockets of leishmanial and human PdxK, rendering LdPdxK an attractive candidate for the designing of novel and specific inhibitors.


    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.,Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxal kinase, putative
A, B
322Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BLM4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BLM4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

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A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
UEG
Query on UEG

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A, B
4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol
C8 H11 N O3
LXNHXLLTXMVWPM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.700α = 90.00
b = 71.690β = 99.28
c = 77.140γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
iMOSFLMdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release