8BR4 | pdb_00008br4

Structure of GAPDH from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 
    0.295 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.257 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Stoichiometry of ligand binding and role of C-terminal lysines in Mycobacterium tuberculosis and human GAPDH multifunctionality.

Kumar, A.Kumar, R.Boradia, V.M.Malhotra, H.Kumar, A.Seth, S.Garg, P.Karthikeyan, S.Raje, M.Iyengar Raje, C.

(2024) FEBS J 

  • DOI: https://doi.org/10.1111/febs.17298
  • Primary Citation of Related Structures:  
    8BR4

  • PubMed Abstract: 

    Glyceraldehyde-3-phosphate-dehydrogenase (GAPDH; EC1.2.1.12) has several functions in Mycobacterium tuberculosis (Mtb) and the human host. Apart from its role in glycolysis, it serves both as a cell surface and a secreted receptor for plasmin(ogen) (Plg/Plm), transferrin (Tf), and lactoferrin (Lf). Plg sequestration by Mtb GAPDH facilitates bacterial adhesion and tissue invasion, while an equivalent interaction with host GAPDH regulates immune cell migration. In both, host and microbe, internalization of Tf/Lf-GAPDH complexes serves as a route for iron acquisition. To date, the structure of Mtb GAPDH or the residues involved in these moonlighting interactions have not been identified. This study provides the first known X-ray crystal structure of Mtb GAPDH. Through further mutagenesis and functional assays, we found that the C-terminal lysines of Mtb and human GAPDH affect enzyme activity and ligand binding. We also establish the stoichiometry of Plg, Tf and Lf interactions with the GAPDH tetramer. Lastly, molecular simulation studies reveal the interactions of the C-terminal lysine residues.


  • Organizational Affiliation
    • Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sahibzada Ajit Singh Nagar, Punjab, India.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
357Mycobacterium tuberculosisMutation(s): 0 
Gene Names: gapMT1480
EC: 1.2.1.12
UniProt
Find proteins for P9WN83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WN83 
Go to UniProtKB:  P9WN83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WN83
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth J]
CA [auth K]
DA [auth L]
EA [auth M]
AA [auth I],
BA [auth J],
CA [auth K],
DA [auth L],
EA [auth M],
FA [auth N],
GA [auth O],
HA [auth P],
Q [auth A],
S [auth B],
T [auth C],
U [auth D],
W [auth E],
X [auth F],
Y [auth G],
Z [auth H]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
R [auth A],
V [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free:  0.295 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.886α = 90
b = 139.166β = 108.52
c = 141.478γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/HRD/NBA/37/01/2014
Department of Biotechnology (DBT, India)IndiaBT/PR13469/BRB/10/1396/2015
Department of Science & Technology (DST, India)IndiaEMR/2016/00/1898

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Database references, Structure summary