2GAR

A PH-DEPENDENT STABLIZATION OF AN ACTIVE SITE LOOP OBSERVED FROM LOW AND HIGH PH CRYSTAL STRUCTURES OF MUTANT MONOMERIC GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A pH-dependent stabilization of an active site loop observed from low and high pH crystal structures of mutant monomeric glycinamide ribonucleotide transformylase at 1.8 to 1.9 A.

Su, Y.Yamashita, M.M.Greasley, S.E.Mullen, C.A.Shim, J.H.Jennings, P.A.Benkovic, S.J.Wilson, I.A.

(1998) J.Mol.Biol. 281: 485-499

  • DOI: 10.1006/jmbi.1998.1931
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A mutation in the dimer interface of Escherichia coli glycinamide ribonucleotide transformylase (GarTfase) disrupts the observed pH-dependent association of the wild-type enzyme, but has no observable effect on the enzyme activity. Here, we assess wh ...

    A mutation in the dimer interface of Escherichia coli glycinamide ribonucleotide transformylase (GarTfase) disrupts the observed pH-dependent association of the wild-type enzyme, but has no observable effect on the enzyme activity. Here, we assess whether a pH effect on the enzyme's conformation is sufficient by itself to explain the pH-dependence of the GarTfase reaction. A pH-dependent conformational change is observed between two high-resolution crystal structures of the Glu70Ala mutant GarTfase at pH 3.5 (1.8 A) and 7.5 (1.9 A). Residues 110 to 131 in GarTfase undergo a transformation from a disordered loop at pH 3.5, where the enzyme is inactive, to an ordered loop-helix structure at pH 7.5, where the enzyme is active. The ordering of this flexible loop-helix has a direct effect on catalytic residues in the active site, binding of the folate cofactor and shielding of the active site from solvent. A main-chain carbonyl oxygen atom from Tyr115 in the ordered loop forms a hydrogen bond with His108, and thereby provides electronic and structural stabilization of this key active site residue. Kinetic data indicate that the pKa of His108 is in fact raised to 9. 2. The loop movement can be correlated with elevation of the His pKa, but with further stabilization, probably from Asp144, after the binding of folate cofactor. Leu118, also in the loop, becomes positioned near the p-amino benzoic acid binding site, providing additional hydrophobic interactions with the cofactor 10-formyl tetrahydrofolate. Thus, the pH-dependence of the enzyme activity appears to arise from local active site rearrangements and not from differences due to monomer-dimer association.


    Related Citations: 
    • Crystal Structure of Glycinamide Ribonucleotide Transformylase from Escherichia Coli at 3.0 A Resolution. A Target Enzyme for Chemotherapy
      Chen, P.,Schulze-Gahmen, U.,Stura, E.A.,Inglese, J.,Johnson, D.L.,Marolewski, A.,Benkovic, S.J.,Wilson, I.A.
      (1992) J.Mol.Biol. 227: 283
    • Structures of Apo and Complexed Escherichia Coli Glycinamide Ribonucleotide Transformylase
      Almassy, R.J.,Janson, C.A.,Kan, C.C.,Hostomska, Z.
      (1992) Proc.Natl.Acad.Sci.USA 89: 6114
    • Towards Structure-Based Drug Design: Crystal Structure of a Multisubstrate Adduct Complex of Glycinamide Ribonucleotide Transformylase at 1.96 A Resolution
      Klein, C.,Chen, P.,Arevalo, J.H.,Stura, E.A.,Marolewski, A.,Warren, M.S.,Benkovic, S.J.,Wilson, I.A.
      (1995) J.Mol.Biol. 249: 153


    Organizational Affiliation

    Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92093-0359, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
A
212Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: purN
EC: 2.1.2.2
Find proteins for P08179 (Escherichia coli (strain K12))
Go to UniProtKB:  P08179
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.800α = 90.00
b = 47.800β = 90.00
c = 107.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
X-PLORphasing
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-12
    Type: Initial release
  • Version 1.1: 2008-03-05
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance