VOOZH about

URL: https://www.rcsb.org/structure/3UJE

⇱ RCSB PDB - 3UJE: Asymmetric complex of human neuron specific enolase-3-PGA/PEP


👁 RCSB PDB
251,806
Structures from the PDB archive
1,068,577
Computed Structure Models (CSM)

 3UJE | pdb_00003uje

Asymmetric complex of human neuron specific enolase-3-PGA/PEP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.191 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation  3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structures of asymmetric complexes of human neuron specific enolase with resolved substrate and product and an analogous complex with two inhibitors indicate subunit interaction and inhibitor cooperativity.

Qin, J.Chai, G.Brewer, J.M.Lovelace, L.L.Lebioda, L.

(2012) J Inorg Biochem 111: 187-194

  • PubMed22437160 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1016/j.jinorgbio.2012.02.011
  • Primary Citation Related Structures: 
    3UCC, 3UCD, 3UJE, 3UJF, 3UJR, 3UJS

  • PubMed Abstract: 

    In the presence of magnesium, enolase catalyzes the dehydration of 2-phospho-d-glycerate (PGA) to phosphoenolpyruvate (PEP) in glycolysis and the reverse reaction in gluconeogensis at comparable rates. The structure of human neuron specific enolase (hNSE) crystals soaked in PGA showed that the enzyme is active in the crystals and produced PEP; conversely soaking in PEP produced PGA. Moreover, the hNSE dimer contains PGA bound in one subunit and PEP or a mixture of PEP and PGA in the other. Crystals soaked in a mixture of competitive inhibitors tartronate semialdehyde phosphate (TSP) and lactic acid phosphate (LAP) showed asymmetry with TSP binding in the same site as PGA and LAP in the PEP site. Kinetic studies showed that the inhibition of NSE by mixtures of TSP and LAP is stronger than predicted for independently acting inhibitors. This indicates that in some cases inhibition of homodimeric enzymes by mixtures of inhibitors ("heteroinhibition") may offer advantages over single inhibitors.


  • Organizational Affiliation
    • Department of Chemistry & Biochemistry, University of South Carolina, Columbia, SC 29208, United States.

Macromolecule Content 

  • Total Structure Weight: 97.71 kDa 
  • Atom Count: 7,186 
  • Modeled Residue Count: 865 
  • Deposited Residue Count: 886 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-enolase
A, B
443Homo sapiensMutation(s): 0 
Gene Names: ENO2
EC: 4.2.1.11
👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for P09104 (Homo sapiens)
Explore P09104 
Go to UniProtKB:  P09104
PHAROS:  P09104
GTEx:  ENSG00000111674 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09104
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2PG
Query on 2PG

Download Ideal Coordinates CCD File 
E [auth A]2-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
GXIURPTVHJPJLF-UWTATZPHSA-N
👁 Image
PEP
Query on PEP

Download Ideal Coordinates CCD File 
I [auth B]PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
👁 Image
TRS
Query on TRS

Download Ideal Coordinates CCD File 
F [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
👁 Image
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
👁 Image
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.602α = 90
b = 119.726β = 90
c = 68.04γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
CNSphasing

Structure Validation

View Full Validation Report

👁 Image


Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.