1A96

XPRTASE FROM E. COLI WITH BOUND CPRPP AND XANTHINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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This is version 1.2 of the entry. See complete history


Literature

Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase.

Vos, S.Parry, R.J.Burns, M.R.de Jersey, J.Martin, J.L.

(1998) J Mol Biol 282: 875-889

  • DOI: 10.1006/jmbi.1998.2051
  • Primary Citation of Related Structures:  
    1A95, 1A96, 1A97, 1A98

  • PubMed Abstract: 
  • Structures of free, substrate-bound and product-bound forms of Escherichia coli xanthine-guanine phosphoribosyltransferase (XGPRT) have been determined by X-ray crystallography. These are compared with the previously determined structure of magnesium and sulphate-bound XPRT ...

    Structures of free, substrate-bound and product-bound forms of Escherichia coli xanthine-guanine phosphoribosyltransferase (XGPRT) have been determined by X-ray crystallography. These are compared with the previously determined structure of magnesium and sulphate-bound XPRT. The structure of free XGPRT at 2.25 A resolution confirms the flexibility of residues in and around a mobile loop identified in other PRTases and shows that the cis-peptide conformation of Arg37 at the active site is maintained in the absence of bound ligands. The structures of XGPRT complexed with the purine base substrates guanine or xanthine in combination with cPRib-PP, an analog of the second substrate PRib-PP, have been solved to 2.0 A resolution. In these two structures the disordered phosphate-binding loop of uncomplexed XGPRT becomes ordered through interactions with the 5'-phosphate group of cPRib-PP. The cyclopentane ring of cPRib-PP has the C3 exo pucker conformation, stabilised by the cPRib-PP-bound Mg2+. The purine base specificity of XGPRT appears to be due to water-mediated interactions between the 2-exocyclic groups of guanine or xanthine and side-chains of Glu136 and Asp140, as well as the main-chain oxygen atom of Ile135. Asp92, together with Lys115, could help stabilise the N7-protonated tautomer of the incoming base and could act as a general base to remove the proton from N7 when the nucleotide product is formed. The 2.6 A resolution structure of XGPRT complexed with product GMP is similar to the substrate-bound complexes. However, the ribose ring of GMP is rotated by approximately 24 degrees compared with the equivalent ring in cPRib-PP. This rotation results in the loss of all interactions between the ribosyl group and the enzyme in the product complex.


    Organizational Affiliation

    Department of Biochemistry, The University of Queensland, Brisbane, Qld 4072, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASEA, B, C, D152Escherichia coliMutation(s): 0 
Gene Names: gpt
EC: 2.4.2.22 (PDB Primary Data), 2.4.2 (UniProt)
UniProt
Find proteins for P0A9M5 (Escherichia coli (strain K12))
Explore P0A9M5 
Go to UniProtKB:  P0A9M5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCP (Subject of Investigation/LOI)
Query on PCP

Download Ideal Coordinates CCD File 
G [auth B], J [auth C]1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE
C6 H15 O13 P3
OICBXEWBKALHHB-MOJAZDJTSA-N
 Ligand Interaction
XAN (Subject of Investigation/LOI)
Query on XAN

Download Ideal Coordinates CCD File 
H [auth B], K [auth C]XANTHINE
C5 H4 N4 O2
LRFVTYWOQMYALW-UHFFFAOYSA-N
 Ligand Interaction
BO3
Query on BO3

Download Ideal Coordinates CCD File 
E [auth A], L [auth D]BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth B], I [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.2α = 90
b = 94.2β = 90
c = 165.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance