4WNC

Crystal structure of human wild-type GAPDH at 1.99 angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.139 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A Dimer Interface Mutation in Glyceraldehyde-3-Phosphate Dehydrogenase Regulates Its Binding to AU-rich RNA.

White, M.R.Khan, M.M.Deredge, D.Ross, C.R.Quintyn, R.Zucconi, B.E.Wysocki, V.H.Wintrode, P.L.Wilson, G.M.Garcin, E.D.

(2015) J Biol Chem 290: 1770-1785

  • DOI: https://doi.org/10.1074/jbc.M114.618165
  • Primary Citation of Related Structures:  
    4WNC, 4WNI

  • PubMed Abstract: 

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an enzyme best known for its role in glycolysis. However, extra-glycolytic functions of GAPDH have been described, including regulation of protein expression via RNA binding. GAPDH binds to numerous adenine-uridine rich elements (AREs) from various mRNA 3'-untranslated regions in vitro and in vivo despite its lack of a canonical RNA binding motif. How GAPDH binds to these AREs is still unknown. Here we discovered that GAPDH binds with high affinity to the core ARE from tumor necrosis factor-α mRNA via a two-step binding mechanism. We demonstrate that a mutation at the GAPDH dimer interface impairs formation of the second RNA-GAPDH complex and leads to changes in the RNA structure. We investigated the effect of this interfacial mutation on GAPDH oligomerization by crystallography, small-angle x-ray scattering, nano-electrospray ionization native mass spectrometry, and hydrogen-deuterium exchange mass spectrometry. We show that the mutation does not significantly affect GAPDH tetramerization as previously proposed. Instead, the mutation promotes short-range and long-range dynamic changes in regions located at the dimer and tetramer interface and in the NAD(+) binding site. These dynamic changes are localized along the P axis of the GAPDH tetramer, suggesting that this region is important for RNA binding. Based on our results, we propose a model for sequential GAPDH binding to RNA via residues located at the dimer and tetramer interfaces.


  • Organizational Affiliation

    From the Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase335Homo sapiensMutation(s): 0 
Gene Names: GAPDHGAPDCDABP0047OK/SW-cl.12
EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P04406 (Homo sapiens)
Explore P04406 
Go to UniProtKB:  P04406
PHAROS:  P04406
GTEx:  ENSG00000111640 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04406
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
I [auth O]
L [auth A]
N [auth B]
P [auth C]
T [auth D]
I [auth O],
L [auth A],
N [auth B],
P [auth C],
T [auth D],
U [auth E]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth O]
M [auth A]
O [auth B]
Q [auth C]
R [auth C]
J [auth O],
M [auth A],
O [auth B],
Q [auth C],
R [auth C],
V [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
K [auth O],
S [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.139 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.537α = 90
b = 81.423β = 90.06
c = 147.802γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-12-03 
  • Deposition Author(s): Garcin, E.D.

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2015-02-11
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description