1PII

THREE-DIMENSIONAL STRUCTURE OF THE BIFUNCTIONAL ENZYME PHOSPHORIBOSYLANTHRANILATE ISOMERASE: INDOLEGLYCEROLPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI REFINED AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 A resolution.

Wilmanns, M.Priestle, J.P.Niermann, T.Jansonius, J.N.

(1992) J Mol Biol 223: 477-507

  • DOI: 10.1016/0022-2836(92)90665-7
  • Primary Citation of Related Structures:  
    1PII

  • PubMed Abstract: 
  • The three-dimensional structure of the monomeric bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from Escherichia coli has been refined at 2.0 A resolution, using oscillation film data obtained from synchrotron radiation ...

    The three-dimensional structure of the monomeric bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from Escherichia coli has been refined at 2.0 A resolution, using oscillation film data obtained from synchrotron radiation. The model includes the complete protein (452 residues), two phosphate ions and 628 water molecules. The final R-factor is 17.3% for all observed data between 15 and 2 A resolution. The root-mean-square deviations from ideal bond lengths and bond angles are 0.010 A and 3.2 degrees, respectively. The structure of N-(5'-phosphoribosyl)anthranilate isomerase: indole-3-glycerol-phosphate synthase from E. coli comprises two beta/alpha-barrel domains that superimpose with a root-mean-square deviation of 2.03 A for 138 C alpha-pairs. The C-terminal domain (residues 256 to 452) catalyses the PRAI reaction and the N-terminal domain (residues 1 to 255) catalyses the IGPS reaction, two sequential steps in tryptophan biosynthesis. The enzyme has the overall shape of a dumb-bell, resulting in a surface area that is considerably larger than normally observed for monomeric proteins of this size. The active sites of the PRAI and the IGPS domains, both located at the C-terminal side of the central beta-barrel, contain equivalent binding sites for the phosphate moieties of the substrates N-(5'-phosphoribosyl) anthranilate and 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate. These two phosphate binding sites are identical with respect to their positions within the tertiary structure of the beta/alpha-barrel, the conformation of the residues involved in phosphate binding and the hydrogen-bonding network between the phosphate ions and the protein. The active site cavities of both domains contain similar hydrophobic pockets that presumably bind the anthranilic acid moieties of the substrates. These similarities of the tertiary structures and the active sites of the two domains provide evidence that N-(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from E. coli results from a gene duplication event of a monomeric beta/alpha-barrel ancestor.


    Related Citations: 
    • Structural Conservation in Parallel Beta(Slash)Alpha-Barrel Enzymes that Catalyze Three Sequential Reactions in the Pathway of Tryptophan Biosynthesis
      Wilmanns, M., Hyde, C.C., Davies, D.R., Kirschner, K., Jansonius, J.N.
      (1991) Biochemistry 30: 9161
    • Three-Dimensional Structure of the Bifunctional Enzyme N-(5'-Phosphoribosyl)Anthranilate Isomerase-Indole-3-Glycerol-Phosphate Synthase from Escherichia Coli
      Priestle, J.P., Gruetter, M.G., White, J.L., Vincent, M.G., Kania, M., Wilson, E., Jardetzky, T.S., Kirschner, K., Jansonius, J.N.
      (1987) Proc Natl Acad Sci U S A 84: 5690
    • Crystallization and Preliminary X-Ray Crystallographic Data of the Bifunctional Enzyme Phosphoribosyl-Anthranilate Isomerase-Indole-3-Glycerol-Phosphate Synthase from Escherichia Coli
      White, J.L., Gruetter, M.G., Wilson, E., Thaller, C., Ford, G.C., Smit, J.D.G., Jansonius, J.N., Kirschner, K.
      (1982) FEBS Lett 148: 87

    Organizational Affiliation

    Department of Structural Biology, University of Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-(5'PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE A452Escherichia coliMutation(s): 0 
EC: 4.1.1.48 (PDB Primary Data), 5.3.1.24 (UniProt)
Find proteins for P00909 (Escherichia coli (strain K12))
Explore P00909 
Go to UniProtKB:  P00909
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.173 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.7α = 90
b = 104.7β = 90
c = 68γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Advisory, Derived calculations, Other