4YWR

Structure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii in non-covalent complex with pyridoxal phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Characterization of an Acinetobacter baumannii Monofunctional Phosphomethylpyrimidine Kinase That Is Inhibited by Pyridoxal Phosphate.

De Vitto, H.Belfon, K.K.J.Sharma, N.Toay, S.Abendroth, J.Dranow, D.M.Lukacs, C.M.Choi, R.Udell, H.S.Willis, S.Barrera, G.Beyer, O.Li, T.D.Hicks, K.A.Torelli, A.T.French, J.B.

(2024) Biochemistry 

  • DOI: https://doi.org/10.1021/acs.biochem.3c00640
  • Primary Citation of Related Structures:  
    4YL5, 4YWR

  • PubMed Abstract: 

    Thiamin and its phosphate derivatives are ubiquitous molecules involved as essential cofactors in many cellular processes. The de novo biosynthesis of thiamin employs the parallel synthesis of 4-methyl-5-(2-hydroxyethyl)thiazole (THZ-P) and 4-amino-2-methyl-5(diphosphooxymethyl) pyrimidine (HMP) pyrophosphate (HMP-PP), which are coupled to generate thiamin phosphate. Most organisms that can biosynthesize thiamin employ a kinase (HMPK or ThiD) to generate HMP-PP. In nearly all cases, this enzyme is bifunctional and can also salvage free HMP, producing HMP-P, the monophosphate precursor of HMP-PP. Here we present high-resolution crystal structures of an HMPK from Acinetobacter baumannii (AbHMPK), both unliganded and with pyridoxal 5-phosphate (PLP) noncovalently bound. Despite the similarity between HMPK and pyridoxal kinase enzymes, our kinetics analysis indicates that AbHMPK accepts HMP exclusively as a substrate and cannot turn over pyridoxal, pyridoxamine, or pyridoxine nor does it display phosphatase activity. PLP does, however, act as a weak inhibitor of AbHMPK with an IC 50 of 768 μM. Surprisingly, unlike other HMPKs, AbHMPK catalyzes only the phosphorylation of HMP and does not generate the diphosphate HMP-PP. This suggests that an additional kinase is present in A. baumannii , or an alternative mechanism is in operation to complete the biosynthesis of thiamin.


  • Organizational Affiliation

    The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase263Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: A591_A3049
UniProt
Find proteins for A0A0J9X285 (Acinetobacter baumannii (strain IS-123))
Explore A0A0J9X285 
Go to UniProtKB:  A0A0J9X285
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9X285
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.82α = 90
b = 108.1β = 90
c = 88.88γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-05-29
    Changes: Database references