6D43 | pdb_00006d43

CHARACTERIZATION OF HUMAN TRIOSEPHOSPHATE ISOMERASE S-NITROSYLATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.256 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6D43

This is version 1.3 of the entry. See complete history

Literature

Characterization of human triosephosphate isomerase S-nitrosylation.

Romero, J.M.Carrizo, M.E.Curtino, J.A.

(2018) Nitric Oxide 77: 26-34

  • DOI: https://doi.org/10.1016/j.niox.2018.04.004
  • Primary Citation Related Structures: 
    6D43

  • PubMed Abstract: 

    Triosephosphate isomerase (TPI), the glycolytic enzyme that catalyzes the isomerization of dihydroxyacetone phosphate (DHAP) to glyceraldehyde-3-phosphate (G3P), has been frequently identified as a target of S-nitrosylation by proteomic studies. However, the effect of S-nitrosylation on its activity has only been explored in plants and algae. Here, we describe the in vitro S-nitrosylation of human TPI (hTPI), and the effect of the modification on its enzymatic parameters. NO-incorporation into the enzyme cysteine residues occurred by a time-dependent S-transnitrosylation from both, S-nitrosocysteine (CySNO) and S-nitrosoglutathione (GSNO), with CySNO being the more efficient NO-donor. Both X-ray crystal structure and mass spectrometry analyses showed that only Cys217 was S-nitrosylated. hTPI S-nitrosylation produced a 30% inhibition of the Vmax of the DHAP conversion to G3P, without affecting the Km for DHAP. This is the first study describing features of human TPI S-nitrosylation.


  • Organizational Affiliation
    • Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, Universidad Nacional de Córdoba - Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET)), Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina. Electronic address: jromero@fcq.unc.edu.ar.

Macromolecule Content 

  • Total Structure Weight: 52.89 kDa 
  • Atom Count: 4,084 
  • Modeled Residue Count: 491 
  • Deposited Residue Count: 492 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Triosephosphate isomerase246Homo sapiensMutation(s): 0 
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Triosephosphate isomerase246Homo sapiensMutation(s): 0 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IPA

Query on IPA



Download:Ideal Coordinates CCD File
C [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SNC
Query on SNC
A
L-PEPTIDE LINKINGC3 H6 N2 O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.256 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.92α = 90
b = 73.98β = 90
c = 93.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Council (NRC, Argentina)ArgentinaPIP 11220120100637CO

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary