3H9E

Crystal structure of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS) complex with NAD and phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

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Literature

Structure and kinetic characterization of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase, GAPDS.

Chaikuad, A.Shafqat, N.Al-Mokhtar, R.Cameron, G.Clarke, A.R.Brady, R.L.Oppermann, U.Frayne, J.Yue, W.W.

(2011) Biochem J 435: 401-409

  • DOI: https://doi.org/10.1042/BJ20101442
  • Primary Citation of Related Structures:  
    3H9E, 3PFW

  • PubMed Abstract: 

    hGAPDS (human sperm-specific glyceraldehyde-3-phosphate dehydrogenase) is a glycolytic enzyme essential for the survival of spermatozoa, and constitutes a potential target for non-hormonal contraception. However, enzyme characterization of GAPDS has been hampered by the difficulty in producing soluble recombinant protein. In the present study, we have overexpressed in Escherichia coli a highly soluble form of hGAPDS truncated at the N-terminus (hGAPDSΔN), and crystallized the homotetrameric enzyme in two ligand complexes. The hGAPDSΔN-NAD+-phosphate structure maps the two anion-recognition sites within the catalytic pocket that correspond to the conserved Ps site and the newly recognized Pi site identified in other organisms. The hGAPDSΔN-NAD+-glycerol structure shows serendipitous binding of glycerol at the Ps and new Pi sites, demonstrating the propensity of these anion-recognition sites to bind non-physiologically relevant ligands. A comparison of kinetic profiles between hGAPDSΔN and its somatic equivalent reveals a 3-fold increase in catalytic efficiency for hGAPDSΔN. This may be attributable to subtle amino acid substitutions peripheral to the active centre that influence the charge properties and protonation states of catalytic residues. Our data therefore elucidate structural and kinetic features of hGAPDS that might provide insightful information towards inhibitor development.


  • Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase, testis-specificA [auth O],
B [auth P]
346Homo sapiensMutation(s): 0 
Gene Names: GAPD2GAPDH2GAPDHSGAPDSHSD-35HSD35
EC: 1.2.1.12
UniProt & NIH Common Fund Data Resources
Find proteins for O14556 (Homo sapiens)
Explore O14556 
Go to UniProtKB:  O14556
PHAROS:  O14556
GTEx:  ENSG00000105679 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14556
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 
C [auth O],
L [auth P]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth O],
E [auth O],
M [auth P],
N [auth P]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth O]
G [auth O]
H [auth O]
I [auth O]
J [auth O]
F [auth O],
G [auth O],
H [auth O],
I [auth O],
J [auth O],
K [auth O],
O [auth P],
P,
Q [auth P],
R [auth P],
S [auth P],
T [auth P],
U [auth P],
V [auth P]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.96α = 90
b = 71.78β = 122.9
c = 81.26γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description