2YYY

Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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This is version 1.2 of the entry. See complete history


Literature

Structure of glyceraldehyde-3-phosphate dehydrogenase from the archaeal hyperthermophile Methanocaldococcus jannaschii.

Malay, A.D.Bessho, Y.Ellis, M.J.Antonyuk, S.V.Strange, R.W.Hasnain, S.S.Shinkai, A.Padmanabhan, B.Yokoyama, S.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1227-1233

  • DOI: https://doi.org/10.1107/S1744309109047046
  • Primary Citation of Related Structures:  
    2YYY

  • PubMed Abstract: 

    The X-ray crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the hyperthermophilic archaeon Methanocaldococcus jannaschii (Mj-GAPDH) was determined to 1.81 A resolution. The crystal belonged to space group C222(1), with unit-cell parameters a = 83.4, b = 152.0, c = 118.6 A. The structure was solved by molecular replacement and was refined to a final R factor of 17.1% (R(free) = 19.8%). The final structure included the cofactor NADP(+) at the nucleotide-binding site and featured unoccupied inorganic and substrate phosphate-binding sites. A comparison with GAPDH structures from mesophilic sources suggested that Mj-GAPDH is stabilized by extensive electrostatic interactions between the C-terminal alpha-helices and various distal loop regions, which are likely to contribute to thermal stability. The key phosphate-binding residues in the active site of Mj-GAPDH are conserved in other archaeal GAPDH proteins. These residues undergo a conformational shift in response to occupancy of the inorganic phosphate site.


  • Organizational Affiliation

    Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase
A, B
343Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
EC: 1.2.1.59
UniProt
Find proteins for Q58546 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58546 
Go to UniProtKB:  Q58546
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58546
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.398α = 90
b = 152.04β = 90
c = 118.552γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description