5AJU

Crystal structure of ligand-free phosphoribohydroxylase lonely guy from Claviceps purpurea in complex with phosphoribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Three-Dimensional Structure of "Lonely Guy" from Claviceps Purpurea Provides Insights Into the Phosphoribohydrolase Function of Rossmann Fold-Containing Lysine Decarboxylase-Like Proteins.

Dzurova, L.Forneris, F.Savino, S.Galuszka, P.Vrabka, J.Frebort, I.

(2015) Proteins 83: 1539

  • DOI: 10.1002/prot.24835
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The recently discovered cytokinin (CK)-specific phosphoribohydrolase "Lonely Guy" (LOG) is a key enzyme of CK biosynthesis, converting inactive CK nucleotides into biologically active free bases. We have determined the crystal structures of LOG from ...

    The recently discovered cytokinin (CK)-specific phosphoribohydrolase "Lonely Guy" (LOG) is a key enzyme of CK biosynthesis, converting inactive CK nucleotides into biologically active free bases. We have determined the crystal structures of LOG from Claviceps purpurea (cpLOG) and its complex with the enzymatic product phosphoribose. The structures reveal a dimeric arrangement of Rossmann folds, with the ligands bound to large pockets at the interface between cpLOG monomers. Structural comparisons highlight the homology of cpLOG to putative lysine decarboxylases. Extended sequence analysis enabled identification of a distinguishing LOG sequence signature. Taken together, our data suggest phosphoribohydrolase activity for several proteins of unknown function.


    Organizational Affiliation

    Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, 783 71, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHORIBOHYDROLASE LONELY GUY
A
274Claviceps purpurea (strain 20.1)Mutation(s): 0 
Find proteins for M1VUY5 (Claviceps purpurea (strain 20.1))
Go to UniProtKB:  M1VUY5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RP5
Query on RP5

Download SDF File 
Download CCD File 
A
5-O-phosphono-beta-D-ribofuranose
[(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE
C5 H11 O8 P
KTVPXOYAKDPRHY-TXICZTDVSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.214 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.970α = 90.00
b = 78.970β = 90.00
c = 144.640γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHASERphasing
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Database references