5AJT

Crystal structure of ligand-free phosphoribohydrolase lonely guy from Claviceps purpurea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 2.0 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: 1539-1546

  • 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

    The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy.,Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy.,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, B, C, D
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
TAR
Query on TAR

Download SDF File 
Download CCD File 
A, B, C, D
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.215 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 82.540α = 90.00
b = 83.170β = 94.03
c = 163.652γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction
PHENIXrefinement

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
  • Version 2.0: 2019-06-26
    Type: Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Other, Structure summary