1KY8

Crystal Structure of the Non-phosphorylating glyceraldehyde-3-phosphate Dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Crystal Structure of the Allosteric Non-phosphorylating glyceraldehyde-3-phosphate Dehydrogenase from the Hyperthermophilic Archaeum Thermoproteus tenax

Pohl, E.Brunner, N.Wilmanns, M.Hensel, R.

(2002) J.Biol.Chem. 277: 19938-19945

  • DOI: 10.1074/jbc.M112244200

  • PubMed Abstract: 
  • The NAD(+)-dependent non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) from the hyperthermophilic archaeum Thermoproteus tenax represents an archaeal member of the diverse superfamily of aldehyde dehydrogenases (ALDHs). GAPN catalyz ...

    The NAD(+)-dependent non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) from the hyperthermophilic archaeum Thermoproteus tenax represents an archaeal member of the diverse superfamily of aldehyde dehydrogenases (ALDHs). GAPN catalyzes the irreversible oxidation of d-glyceraldehyde 3-phosphate to 3-phosphoglycerate. In this study, we present the crystal structure of GAPN in complex with its natural inhibitor NADP(+) determined by multiple anomalous diffraction methods. The structure was refined to a resolution of 2.4 A with an R-factor of 0.21. The overall fold of GAPN is similar to the structures of ALDHs described previously, consisting of three domains: a nucleotide-binding domain, a catalytic domain, and an oligomerization domain. Local differences in the active site are responsible for substrate specificity. The inhibitor NADP(+) binds at an equivalent site to the cosubstrate-binding site of other ALDHs and blocks the enzyme in its inactive state, possibly preventing the transition to the active conformation. Structural comparison between GAPN from the hyperthermophilic T. tenax and homologs of mesophilic organisms establishes several characteristics of thermostabilization. These include protection against heat-induced covalent modifications by reducing and stabilizing labile residues, a decrease in number and volume of empty cavities, an increase in beta-strand content, and a strengthening of subunit contacts by ionic and hydrophobic interactions.


    Organizational Affiliation

    European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22603 Hamburg, Germany. ehmke@embl-hamburg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glyceraldehyde-3-phosphate dehydrogenase
A
501Thermoproteus tenaxGene Names: gapN
EC: 1.2.1.90
Find proteins for O57693 (Thermoproteus tenax)
Go to UniProtKB:  O57693
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NAPKd: 1000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.208 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 185.200α = 90.00
b = 185.200β = 90.00
c = 132.100γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
X-PLORrefinement
SHELXmodel building
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation