1FS5

A DISCOVERY OF THREE ALTERNATE CONFORMATIONS IN THE ACTIVE SITE OF GLUCOSAMINE-6-PHOSPHATE ISOMERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural flexibility, an essential component of the allosteric activation in Escherichia coli glucosamine-6-phosphate deaminase.

Rudino-Pinera, E.Morales-Arrieta, S.Rojas-Trejo, S.P.Horjales, E.

(2002) Acta Crystallogr.,Sect.D 58: 10-20

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A new crystallographic structure of the free active-site R conformer of the allosteric enzyme glucosamine-6-phosphate deaminase from Escherichia coli, coupled with previously reported structures of the T and R conformers, generates a detailed descrip ...

    A new crystallographic structure of the free active-site R conformer of the allosteric enzyme glucosamine-6-phosphate deaminase from Escherichia coli, coupled with previously reported structures of the T and R conformers, generates a detailed description of the heterotropic allosteric transition in which structural flexibility plays a central role. The T conformer's external zone [Horjales et al. (1999), Structure, 7, 527-536] presents higher B values than in the R conformers. The ligand-free enzyme (T conformer) undergoes an allosteric transition to the free active-site R conformer upon binding of the allosteric activator. This structure shows three alternate conformations of the mobile section of the active-site lid (residues 163-182), in comparison to the high B values for the unique conformation of the T conformer. One of these alternate R conformations corresponds to the active-site lid found when the substrate is bound. The disorder associated with the three alternate conformations can be related to the biological regulation of the K(m) of the enzyme for the reaction, which is metabolically required to maintain adequate concentrations of the activator, which holds the enzyme in its R state. Seven alternate conformations for the active-site lid and three for the C-terminus were refined for the T structure using isotropic B factors. Some of these conformers approach that of the R conformer in geometry. Furthermore, the direction of the atomic vibrations obtained with anisotropic B refinement supports the hypothesis of an oscillating rather than a tense T state. The concerted character of the allosteric transition is also analysed in view of the apparent dynamics of the conformers.


    Related Citations: 
    • Structure and catalytic mechanism of glucosamine-6-phosphate deaminase from Escherichia coli at 2.1A resolution
      Oliva, G.,Fontes, M.R.M.,Garratt, R.C.,Altamirano, M.M.,Calcagno, M.L.,Horjales, E.
      (1995) Structure 3: 1323
    • The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3A resolution
      Horjales, E.,Altamirano, M.M.,Calcagno, M.L.,Garratt, R.C.,Oliva, G.
      (1999) Structure 7: 527


    Organizational Affiliation

    Departamento de Reconocimiento Molecular y Bioestructura, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, PO Box 510-3, Cuernavaca, MOR 62271, Mexico. rudino@ibt.unam.mx




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOSAMINE-6-PHOSPHATE DEAMINASE
A, B
266Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nagB (glmD)
EC: 3.5.99.6
Find proteins for P0A759 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A759
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download SDF File 
Download CCD File 
A
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
16G
Query on 16G

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
C8 H16 N O9 P
BRGMHAYQAZFZDJ-PVFLNQBWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.212 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 124.228α = 90.00
b = 124.228β = 90.00
c = 222.724γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
DENZOdata reduction
CCP4data scaling
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description