Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with GMP

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

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Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies.

Chittori, S.Simanshu, D.K.Banerjee, S.Murthy, A.M.V.Mathivanan, S.Savithri, H.S.Murthy, M.R.N.

(2013) Biochim Biophys Acta 1834: 2036-2044

  • DOI: https://doi.org/10.1016/j.bbapap.2013.05.020
  • Primary Citation of Related Structures:  
    4FWK, 4FWL, 4FWM, 4FWN, 4FWO, 4FWP, 4FWQ, 4FWR, 4FWS

  • PubMed Abstract: 

    Short-chain fatty acids (SCFAs) play a major role in carbon cycle and can be utilized as a source of carbon and energy by bacteria. Salmonella typhimurium propionate kinase (StTdcD) catalyzes reversible transfer of the γ-phosphate of ATP to propionate during l-threonine degradation to propionate. Kinetic analysis revealed that StTdcD possesses broad ligand specificity and could be activated by various SCFAs (propionate>acetate≈butyrate), nucleotides (ATP≈GTP>CTP≈TTP; dATP>dGTP>dCTP) and metal ions (Mg(2+)≈Mn(2+)>Co(2+)). Inhibition of StTdcD by tricarboxylic acid (TCA) cycle intermediates such as citrate, succinate, α-ketoglutarate and malate suggests that the enzyme could be under plausible feedback regulation. Crystal structures of StTdcD bound to PO4 (phosphate), AMP, ATP, Ap4 (adenosine tetraphosphate), GMP, GDP, GTP, CMP and CTP revealed that binding of nucleotide mainly involves hydrophobic interactions with the base moiety and could account for the broad biochemical specificity observed between the enzyme and nucleotides. Modeling and site-directed mutagenesis studies suggest Ala88 to be an important residue involved in determining the rate of catalysis with SCFA substrates. Molecular dynamics simulations on monomeric and dimeric forms of StTdcD revealed plausible open and closed states, and also suggested role for dimerization in stabilizing segment 235-290 involved in interfacial interactions and ligand binding. Observation of an ethylene glycol molecule bound sufficiently close to the γ-phosphate in StTdcD complexes with triphosphate nucleotides supports direct in-line phosphoryl transfer.

  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India. Electronic address: sagar@mbu.iisc.ernet.in.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Propionate kinase415Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: oxd-2STM3242tdcD
Find proteins for O06961 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore O06961 
Go to UniProtKB:  O06961
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06961
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.921α = 90
b = 110.921β = 90
c = 66.789γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2014-01-29
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description