1GPD

STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Studies of asymmetry in the three-dimensional structure of lobster D-glyceraldehyde-3-phosphate dehydrogenase.

Moras, D.Olsen, K.W.Sabesan, M.N.Buehner, M.Ford, G.C.Rossmann, M.G.

(1975) J.Biol.Chem. 250: 9137-9162


  • PubMed Abstract: 
  • An improved electron density map of lobster holo-D-glyceraldehyde-3-phosphate dehydrogenase has been computed to 2.9 A resolution based on two heavy atom isomorphous derivatives. This has been averaged only over the Q molecular 2-fold axis, which is ...

    An improved electron density map of lobster holo-D-glyceraldehyde-3-phosphate dehydrogenase has been computed to 2.9 A resolution based on two heavy atom isomorphous derivatives. This has been averaged only over the Q molecular 2-fold axis, which is known to be exact in the human holoenzyme. The map showed possible asymmetry between the subunits in which the active centers are closely related across the R axis (that is, between the red and green or between the yellow and blue subunits). A difference map between the electron density of citrate and sulfate-soaked crystals gave further evidence for possible asymmetry. The major differences of electron density between R axis-related subunits appear around the active center and suggest the following interpretations. 1. The conformation of the adenine about the glycosidic bond is the more frequently observed anti with a C-2' endo conformation for the ribose ring in the red and yellow subunits, but is probably syn with a C-3' endo conformation in the green and blue subunits.2. The adenine ribose has its 3'-hydroxyl group hydrogen-bonded to a main chain carbonyl group in the red and yellow subunits but not in the green and blue subunits, as a consequence of the differing ribose conformations. 3. Cysteine-149 is more closely associated with histidine-176 in the green and blue subunits, and appears nearer the nicotinamide in the red and yellow subunits.


    Related Citations: 
    • D-Glyceraldehyde-3-Phosphate Dehydrogenase,Three Dimensional Structure and Evolutionary Significance
      Buehner, M.,Ford, G.C.,Moras, D.,Olsen, K.W.,Rossmann, M.G.
      (1973) Proc.Natl.Acad.Sci.USA 70: 3052
    • Three-Dimensional Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase
      Buehner, M.,Ford, G.C.,Moras, D.,Olsen, K.W.,Rossmann, M.G.
      (1974) J.Mol.Biol. 90: 25
    • Anion Binding Sites in the Active Center of D-Glyceraldehyde-3-Phosphate Dehydrogenase
      Olsen, K.W.,Garavito, R.M.,Sabesan, M.N.,Rossmann, M.G.
      (1976) J.Mol.Biol. 107: 571
    • Sequence Variability and Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase
      Olsen, K.W.,Moras, D.,Rossmann, M.G.,Harris, J.I.
      (1975) J.Biol.Chem. 250: 9313
    • An Application of the Molecular Replacement Technique in Direct Space to a Known Protein Structure
      Argos, P.,Ford, G.C.,Rossmann, M.G.
      (1975) Acta Crystallogr.,Sect.A 31: 499
    • Structure Determination of Crystalline Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase
      Buehner, M.,Ford, G.C.,Moras, D.,Olsen, K.W.,Rossmann, M.G.
      (1974) J.Mol.Biol. 82: 563
    • A Comparison of the Binding and Function of Nad with Respect to Lactate Dehydrogenase and Glyceraldehyde-3-Phosphate Dehydrogenase
      Rossmann, M.G.
      (1975) STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN --: 353
    • Studies on Coenzyme Binding to Glyceraldehyde-3-Phosphate Dehydrogenase
      Olsen, K.W.,Garavito, R.M.,Sabesan, M.N.,Rossmann, M.G.
      (1976) J.Mol.Biol. 107: 577



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
G, R
334Homarus americanusEC: 1.2.1.12
Find proteins for P00357 (Homarus americanus)
Go to UniProtKB:  P00357
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
R
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
G, R
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
G, R
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 149.000α = 90.00
b = 139.100β = 90.00
c = 80.700γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1977-02-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2014-10-29
    Type: Derived calculations