9DV9 | pdb_00009dv9

The AMP-bound structure of AckA from Treponema vincentii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.162 (Depositor), 0.162 (DCC) 
  • R-Value Work: 
    0.140 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.141 (Depositor) 

Starting Model: in silico
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Literature

Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes.

Deka, R.K.Tso, S.C.Liu, W.Z.Brautigam, C.A.

(2025) PLoS One 20: e0312642-e0312642

  • DOI: https://doi.org/10.1371/journal.pone.0312642
  • Primary Citation of Related Structures:  
    9DV8, 9DV9

  • PubMed Abstract: 

    Unraveling the metabolism of Treponema pallidum is a key component to understanding the pathogenesis of the human disease that it causes, syphilis. For decades, it was assumed that glucose was the sole carbon/energy source for this parasitic spirochete. But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway in T. pallidum and related treponemal species. In this hypothetical pathway, exogenous D-lactate can be utilized by the bacterium as an alternative energy source. Herein, we examined the final enzyme in this pathway, acetate kinase (named TP0476), which ostensibly catalyzes the generation of ATP from ADP and acetyl-phosphate. We found that TP0476 was able to carry out this reaction, but the protein was not suitable for biophysical and structural characterization. We thus performed additional studies on the homologous enzyme (75% amino-acid sequence identity) from the oral pathogen Treponema vincentii, TV0924. This protein also exhibited acetate kinase activity, and it was amenable to structural and biophysical studies. We established that the enzyme exists as a dimer in solution, and then determined its crystal structure at a resolution of 1.36 Å, showing that the protein has a similar fold to other known acetate kinases. Mutation of residues in the putative active site drastically altered its enzymatic activity. A second crystal structure of TV0924 in the presence of AMP (at 1.3 Å resolution) provided insight into the binding of one of the enzyme's substrates. On balance, this evidence strongly supported the roles of TP0476 and TV0924 as acetate kinases, reinforcing the hypothesis of an acetogenic pathway in pathogenic treponemes.


  • Organizational Affiliation

    Department of Microbiology, UT Southwestern Medical Center, Dallas, TX, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetate kinase475Treponema pallidumMutation(s): 0 
Gene Names: ackATREVI0001_0924
EC: 2.7.2.1
UniProt
Find proteins for C8PR54 (Treponema vincentii ATCC 35580)
Explore C8PR54 
Go to UniProtKB:  C8PR54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC8PR54
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.162 (Depositor), 0.162 (DCC) 
  • R-Value Work:  0.140 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.102α = 90
b = 105.232β = 90
c = 52.735γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI56305

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release