Crystal structure of Porphyromonas gingivalis phosphotransacetylase in complex with acetyl-CoA

Experimental Data Snapshot

  • Resolution: 2.04 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production inPorphyromonas gingivalis.

Yoshida, Y.Sato, M.Nonaka, T.Hasegawa, Y.Kezuka, Y.

(2019) J Oral Microbiol 11: 1588086-1588086

  • DOI: https://doi.org/10.1080/20002297.2019.1588086
  • Primary Citation of Related Structures:  
    6IOW, 6IOX, 6IOY

  • PubMed Abstract: 

    Acetyl phosphate (AcP) is generally produced from acetyl coenzyme A by phosphotransacetylase (Pta), and subsequent reaction with ADP, catalyzed by acetate kinase (Ack), produces ATP. The mechanism of ATP production in Porphyromonas gingivalis is poorly understood. The aim of this study was to explore the molecular basis of the Pta-Ack pathway in this microorganism. Pta and Ack from P. gingivalis ATCC 33277 were enzymatically and structurally characterized. Structural and mutational analyses suggest that Pta is a dimer with two substrate-binding sites in each subunit. Ack is also dimeric, with a catalytic cleft in each subunit, and structural analysis indicates a dramatic domain motion that opens and closes the cleft during catalysis. ATP formation by Ack proceeds via a sequential mechanism. Reverse transcription-PCR analysis demonstrated that the pta ( PGN_1179 ) and ack ( PGN_1178 ) genes, tandemly located in the genome, are cotranscribed as an operon. Inactivation of pta or ack in P. gingivalis by homologous recombination was successful only when the inactivated gene was expressed in trans . Therefore, both pta and ack genes are essential for this microorganism. Insights into the Pta-Ack pathway reported herein would be helpful to understand the energy acquisition in P. gingivalis .

  • Organizational Affiliation

    Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
340Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: PGN_1179
Find proteins for B2RK03 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RK03 
Go to UniProtKB:  B2RK03
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RK03
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.04 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.693α = 90
b = 130.023β = 90
c = 52.602γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP16K11485
Japan Society for the Promotion of ScienceJapanJP17K11634

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description