8OHA

Crystal structure of Leptospira interrogans GAPDH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

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Ligand Structure Quality Assessment 


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Literature

The structure of Leptospira interrogans GAPDH sheds light into an immunoevasion factor that can target the anaphylatoxin C5a of innate immunity.

Navas-Yuste, S.de la Paz, K.Querol-Garcia, J.Gomez-Quevedo, S.Rodriguez de Cordoba, S.Fernandez, F.J.Vega, M.C.

(2023) Front Immunol 14: 1190943-1190943

  • DOI: https://doi.org/10.3389/fimmu.2023.1190943
  • Primary Citation of Related Structures:  
    8OHA

  • PubMed Abstract: 

    Leptospirosis is a neglected worldwide zoonosis involving farm animals and domestic pets caused by the Gram-negative spirochete Leptospira interrogans . This bacterium deploys a variety of immune evasive mechanisms, some of them targeted at the complement system of the host's innate immunity. In this work, we have solved the X-ray crystallographic structure of L. interrogans glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to 2.37-Å resolution, a glycolytic enzyme that has been shown to exhibit moonlighting functions that potentiate infectivity and immune evasion in various pathogenic organisms. Besides, we have characterized the enzyme's kinetic parameters toward the cognate substrates and have proven that the two natural products anacardic acid and curcumin are able to inhibit L. interrogans GAPDH at micromolar concentration through a noncompetitive inhibition modality. Furthermore, we have established that L. interrogans GAPDH can interact with the anaphylatoxin C5a of human innate immunity in vitro using bio-layer interferometry and a short-range cross-linking reagent that tethers free thiol groups in protein complexes. To shed light into the interaction between L. interrogans GAPDH and C5a, we have also carried out cross-link guided protein-protein docking. These results suggest that L. interrogans could be placed in the growing list of bacterial pathogens that exploit glycolytic enzymes as extracellular immune evasive factors. Analysis of the docking results indicates a low affinity interaction that is consistent with previous evidence, including known binding modes of other α-helical proteins with GAPDH. These findings allow us to propose L. interrogans GAPDH as a potential immune evasive factor targeting the complement system.


  • Organizational Affiliation

    Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase
A, B, C, D, F
A, B, C, D, F, G, H
337Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130Mutation(s): 0 
Gene Names: gapA
UniProt
Find proteins for Q72QM3 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130))
Explore Q72QM3 
Go to UniProtKB:  Q72QM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72QM3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase337Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130Mutation(s): 0 
Gene Names: gapA
UniProt
Find proteins for Q72QM3 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130))
Explore Q72QM3 
Go to UniProtKB:  Q72QM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72QM3
Sequence Annotations
Expand
  • 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 
AB [auth F]
BB [auth G]
GA [auth B]
HB [auth H]
LA [auth C]
AB [auth F],
BB [auth G],
GA [auth B],
HB [auth H],
LA [auth C],
S [auth A],
VA [auth D],
YA [auth E]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CB [auth H]
I [auth A]
J [auth A]
NA [auth D]
V [auth B]
CB [auth H],
I [auth A],
J [auth A],
NA [auth D],
V [auth B],
W [auth B],
X [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
EA [auth B],
FA [auth B],
R [auth A],
UA [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
DB [auth H]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
DB [auth H],
EB [auth H],
FB [auth H],
GB [auth H],
HA [auth C],
IA [auth C],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
M [auth A],
MA [auth D],
N [auth A],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth D],
RA [auth D],
SA [auth D],
T [auth A],
TA [auth D],
U [auth A],
WA [auth E],
XA [auth E],
Y [auth B],
Z [auth B],
ZA [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A, B, C, D, F
A, B, C, D, F, G, H
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.804α = 94.02
b = 82.039β = 95.15
c = 123.182γ = 112.52
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainRTI2018-102242-B-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2019-104912RB-I00
Autonomous Community of MadridSpainS2017/BMD-3673
Autonomous Community of MadridSpainS2022/BMD-7278
Spanish National Research CouncilSpainSGL2103020
Spanish Ministry of Science, Innovation, and UniversitiesSpainSAF2016-81876-REDT

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release