8OHA | pdb_00008oha

Crystal structure of Leptospira interrogans GAPDH

PDB DOI: https://doi.org/10.2210/pdb8OHA/pdb

Classification: HYDROLASE
Organism(s): Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-20 Released: 2023-08-23
Deposition Author(s): Navas-Yuste, S., de la Paz, K., Querol-Garcia, J., Gomez-Quevedo, S., Rodriguez de Cordoba, S., Fernandez, F.J., Vega, M.C.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities, Autonomous Community of Madrid, Spanish National Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.234 (Depositor), 0.226 (DCC)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

PubMed: 37409124 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fimmu.2023.1190943
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 304.28 kDa
Atom Count: 21,537
Modeled Residue Count: 2,674
Deposited Residue Count: 2,696
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D, F A, B, C, D, F, G, H	337	Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130	Mutation(s): 0 Gene Names: gapA EC: 1.2.1
UniProt
Find proteins for Q72QM3 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)) Explore Q72QM3 Go to UniProtKB: Q72QM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72QM3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	E	337	Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130	Mutation(s): 0 Gene Names: gapA EC: 1.2.1
UniProt
Find proteins for Q72QM3 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)) Explore Q72QM3 Go to UniProtKB: Q72QM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72QM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BB [auth G] SDF format, chain GA [auth B] SDF format, chain HB [auth H] SDF format, chain LA [auth C] SDF format, chain S [auth A] SDF format, chain VA [auth D] SDF format, chain YA [auth E] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth G] MOL2 format, chain GA [auth B] MOL2 format, chain HB [auth H] MOL2 format, chain LA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain YA [auth E] mmCIF format, chain AB [auth F] mmCIF format, chain BB [auth G] mmCIF format, chain GA [auth B] mmCIF format, chain HB [auth H] mmCIF format, chain LA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain YA [auth E]	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		Interactions Focus chain AB [auth F] Focus chain BB [auth G] Focus chain GA [auth B] Focus chain HB [auth H] Focus chain LA [auth C] Focus chain S [auth A] Focus chain VA [auth D] Focus chain YA [auth E] Interactions & Density Focus chain AB [auth F] Focus chain BB [auth G] Focus chain GA [auth B] Focus chain HB [auth H] Focus chain LA [auth C] Focus chain S [auth A] Focus chain VA [auth D] Focus chain YA [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CB [auth H] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain NA [auth D] MOL2 format, chain CB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain NA [auth D] mmCIF format, chain CB [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain NA [auth D]	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		Interactions Focus chain CB [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain NA [auth D] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain CB [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain NA [auth D] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain R [auth A] SDF format, chain UA [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain UA [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain UA [auth D]	EA [auth B], FA [auth B], R [auth A], UA [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain R [auth A] Focus chain UA [auth D] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain R [auth A] Focus chain UA [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain DB [auth H] SDF format, chain EB [auth H] SDF format, chain FB [auth H] SDF format, chain GB [auth H] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain U [auth A] SDF format, chain WA [auth E] SDF format, chain XA [auth E] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain ZA [auth F] SDF format, chain JA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth H] MOL2 format, chain EB [auth H] MOL2 format, chain FB [auth H] MOL2 format, chain GB [auth H] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth F] MOL2 format, chain JA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth H] mmCIF format, chain EB [auth H] mmCIF format, chain FB [auth H] mmCIF format, chain GB [auth H] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth A] mmCIF format, chain WA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth F] mmCIF format, chain JA [auth C]	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		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth H] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain GB [auth H] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth H] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain GB [auth H] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B, C, D, F A, B, C, D, F, G, H	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.234 (Depositor), 0.226 (DCC)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.804	α = 94.02
b = 82.039	β = 95.15
c = 123.182	γ = 112.52

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-23

Deposition Author(s):

Rodriguez de Cordoba, S.

Fernandez, F.J.

Vega, M.C.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	RTI2018-102242-B-I00
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2019-104912RB-I00
Autonomous Community of Madrid	Spain	S2017/BMD-3673
Autonomous Community of Madrid	Spain	S2022/BMD-7278
Spanish National Research Council	Spain	SGL2103020
Spanish Ministry of Science, Innovation, and Universities	Spain	SAF2016-81876-REDT