6NLH

Structure of human triose phosphate isomerase R189A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Missense variant in TPI1 (Arg189Gln) causes neurologic deficits through structural changes in the triosephosphate isomerase catalytic site and reduced enzyme levels in vivo.

Roland, B.P.Richards, K.R.Hrizo, S.L.Eicher, S.Barile, Z.J.Chang, T.C.Savon, G.Bianchi, P.Fermo, E.Ricerca, B.M.Tortorolo, L.Vockley, J.VanDemark, A.P.Palladino, M.J.

(2019) Biochim Biophys Acta Mol Basis Dis 1865: 2257-2266

  • DOI: https://doi.org/10.1016/j.bbadis.2019.05.002
  • Primary Citation of Related Structures:  
    6NLH

  • PubMed Abstract: 

    Mutations in the gene triosephosphate isomerase (TPI) lead to a severe multisystem condition that is characterized by hemolytic anemia, a weakened immune system, and significant neurologic symptoms such as seizures, distal neuropathy, and intellectual disability. No effective therapy is available. Here we report a compound heterozygous patient with a novel TPI pathogenic variant (NM_000365.5:c.569G>A:p.(Arg189Gln)) in combination with the common (NM_000365.5:c.315G>C:p.(Glu104Asp)) allele. We characterized the novel variant by mutating the homologous Arg in Drosophila using a genomic engineering system, demonstrating that missense mutations at this position cause a strong loss of function. Compound heterozygote animals were generated and exhibit motor behavioural deficits and markedly reduced protein levels. Furthermore, examinations of the TPI Arg189Gln /TPI Glu104Asp patient fibroblasts confirmed the reduction of TPI levels, suggesting that Arg189Gln may also affect the stability of the protein. The Arg189 residue participates in two salt bridges on the backside of the TPI enzyme dimer, and we reveal that a mutation at this position alters the coordination of the substrate-binding site and important catalytic residues. Collectively, these data reveal a new human pathogenic variant associated with TPI deficiency, identify the Arg189 salt bridge as critical for organizing the catalytic site of the TPI enzyme, and demonstrates that reduced TPI levels are associated with human TPI deficiency. These findings advance our understanding of the molecular pathogenesis of the disease, and suggest new therapeutic avenues for pre-clinical trials.


  • Organizational Affiliation

    Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Triosephosphate isomerase245Homo sapiensMutation(s): 1 
Gene Names: TPI1TPI
EC: 5.3.1.1 (PDB Primary Data), 4.2.3.3 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P60174 (Homo sapiens)
Explore P60174 
Go to UniProtKB:  P60174
PHAROS:  P60174
GTEx:  ENSG00000111669 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60174
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
DA [auth F],
JA [auth H],
N [auth E],
W [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
BR
Query on BR

Download Ideal Coordinates CCD File 
CA [auth F],
IA [auth H],
M [auth E],
V [auth C]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
EA [auth G]
FA [auth G]
GA [auth H]
AA [auth F],
BA [auth F],
EA [auth G],
FA [auth G],
GA [auth H],
HA [auth H],
I [auth A],
J [auth A],
K [auth A],
L [auth E],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth C],
T [auth C],
U [auth C],
X [auth D],
Y [auth D],
Z [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.142α = 90.03
b = 73.661β = 90.03
c = 92.842γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM103369

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description