5VJN | pdb_00005vjn

Crystal Structure of Adenine Phosphoribosyltransferase from Saccharomyces cerevisiae Complexed with D-2,5-Dideoxy-2,5-Imino-Altritol 1,6-Bisphosphate (D-DIAB) and Adenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.266 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Synthesis of bis-Phosphate Iminoaltritol Enantiomers and Structural Characterization with Adenine Phosphoribosyltransferase.

Harris, L.D.Harijan, R.K.Ducati, R.G.Evans, G.B.Hirsch, B.M.Schramm, V.L.

(2018) ACS Chem Biol 13: 152-160

  • DOI: https://doi.org/10.1021/acschembio.7b00601
  • Primary Citation Related Structures: 
    5VJN, 5VJP

  • PubMed Abstract: 

    Phosphoribosyl transferases (PRTs) are essential in nucleotide synthesis and salvage, amino acid, and vitamin synthesis. Transition state analysis of several PRTs has demonstrated ribocation-like transition states with a partial positive charge residing on the pentose ring. Core chemistry for synthesis of transition state analogues related to the 5-phospho-α-d-ribosyl 1-pyrophosphate (PRPP) reactant of these enzymes could be developed by stereospecific placement of bis-phosphate groups on an iminoaltritol ring. Cationic character is provided by the imino group and the bis-phosphates anchor both the 1- and 5-phosphate binding sites. We provide a facile synthetic path to these molecules. Cyclic-nitrone redox methodology was applied to the stereocontrolled synthesis of three stereoisomers of a selectively monoprotected diol relevant to the synthesis of transition-state analogue inhibitors. These polyhydroxylated pyrrolidine natural product analogues were bis-phosphorylated to generate analogues of the ribocationic form of 5-phosphoribosyl 1-phosphate. A safe, high yielding synthesis of the key intermediate represents a new route to these transition state mimics. An enantiomeric pair of iminoaltritol bis-phosphates (L-DIAB and D-DIAB) was prepared and shown to display inhibition of Plasmodium falciparum orotate phosphoribosyltransferase and Saccharomyces cerevisiae adenine phosphoribosyltransferase (ScAPRT). Crystallographic inhibitor binding analysis of L- and D-DIAB bound to the catalytic sites of ScAPRT demonstrates accommodation of both enantiomers by altered ring geometry and bis-phosphate catalytic site contacts.


  • Organizational Affiliation
    • The Ferrier Research Institute, Victoria University of Wellington , 69 Gracefield Rd, Lower Hutt, 5010, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 42.33 kDa 
  • Atom Count: 3,089 
  • Modeled Residue Count: 345 
  • Deposited Residue Count: 374 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adenine phosphoribosyltransferase 1
A, B
187Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: APT1YML022W
EC: 2.4.2.7
UniProt
Find proteins for P49435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49435 
Go to UniProtKB:  P49435
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49435
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IR8

Query on IR8



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
[(2R,3S,4R,5R)-3,4-dihydroxypyrrolidine-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)]
C6 H15 N O10 P2
JDMJAXIARMVOFV-KAZBKCHUSA-N
ADE

Query on ADE



Download:Ideal Coordinates CCD File
G [auth A]ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.266 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.63α = 90
b = 49.8β = 131.04
c = 96.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM41916

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description