Crystal Structure of a Clostridial Dehydrogenase at 2.55 Angstroems Resolution

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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The Antimicrobials Anacardic Acid and Curcumin Are Not-Competitive Inhibitors of Gram-Positive Bacterial Pathogenic Glyceraldehyde-3-Phosphate Dehydrogenase by a Mechanism Unrelated to Human C5a Anaphylatoxin Binding.

Gomez, S.Querol-Garcia, J.Sanchez-Barron, G.Subias, M.Gonzalez-Alsina, A.Franco-Hidalgo, V.Alberti, S.Rodriguez de Cordoba, S.Fernandez, F.J.Vega, M.C.

(2019) Front Microbiol 10: 326-326

  • DOI: https://doi.org/10.3389/fmicb.2019.00326
  • Primary Citation of Related Structures:  
    6FZH, 6FZI

  • PubMed Abstract: 

    The ubiquitous and highly abundant glycolytic enzyme D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is pivotal for the energy and carbon metabolism of most organisms, including human pathogenic bacteria. For bacteria that depend mostly on glycolysis for survival, GAPDH is an attractive target for inhibitor discovery. The availability of high-resolution structures of GAPDH from various pathogenic bacteria is central to the discovery of new antibacterial compounds. We have determined the X-ray crystal structures of two new GAPDH enzymes from Gram-positive bacterial pathogens, Streptococcus pyogenes and Clostridium perfringens . These two structures, and the recent structure of Atopobium vaginae GAPDH, reveal details in the active site that can be exploited for the design of novel inhibitors based on naturally occurring molecules. Two such molecules, anacardic acid and curcumin, have been found to counter bacterial infection in clinical settings, although the cellular targets responsible for their antimicrobial properties remain unknown. We show that both anacardic acid and curcumin inhibit GAPDH from two bacterial pathogens through uncompetitive and non-competitive mechanisms, suggesting GAPDH as a relevant pharmaceutical target for antibacterial development. Inhibition of GAPDH by anacardic acid and curcumin seems to be unrelated to the immune evasion function of pathogenic bacterial GAPDH, since neither natural compound interfere with binding to the human C5a anaphylatoxin.

  • Organizational Affiliation

    Center for Biological Research, Spanish National Research Council, Madrid, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase
A, B, C, D
332Clostridium perfringens SM101Mutation(s): 0 
Gene Names: gapCPR_1301
EC: 1.2.1
Find proteins for Q0STD4 (Clostridium perfringens (strain SM101 / Type A))
Explore Q0STD4 
Go to UniProtKB:  Q0STD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0STD4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
U [auth C],
Z [auth D]
C21 H27 N7 O14 P2
Query on PEG

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J [auth A],
O [auth B]
C4 H10 O3
Query on GOL

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AA [auth D]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
AA [auth D],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
C3 H8 O3
Query on ACT

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BA [auth D]
CA [auth D]
DA [auth D]
K [auth A]
P [auth B]
BA [auth D],
CA [auth D],
DA [auth D],
K [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.28α = 90
b = 101.61β = 107.07
c = 92.82γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Instituto de Salud Carlos IIISpainPI12/01667
Spanish Ministry of Economy and CompetitivenessSpainCTQ2015-66206-C2-2-R
Spanish Ministry of Economy and CompetitivenessSpainSAF2015-72961-EXP
Spanish Network of Excellence on ComplementSpainSAF2016-81876-REDT
Regional Government of MadridSpainS2010/BD-2316
Regional Government of MadridSpainS2017/BMD-3673
European Commission, FP7 ProgrammeBelgiumComplexINC (Contract No. 279039)

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release