Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.75 kDa 
• Atom Count: 6862 
• Residue Count: 868 
• Unique protein chains: 1

5AJT

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

• DOI: 10.2210/pdb5AJT/pdb

• Classification: HYDROLASE
• Organism(s): Claviceps purpurea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-27 Released: 2015-06-03 
• Deposition Author(s): Dzurova, L., Savino, S., Forneris, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.240 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 

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

• PubMed: 26010010 
• DOI: 10.1002/prot.24835
• Primary Citation of Related Structures:  
  5AJU, 5AJT


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOHYDROLASE LONELY GUY	A, B, C, D	274	Claviceps purpurea	Mutation(s): 0
Find proteins for M1VUY5 (Claviceps purpurea (strain 20.1)) Explore M1VUY5  Go to UniProtKB:  M1VUY5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAR	A, B, C, D	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N
EDO	A, B, C, D	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.240 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.54	α = 90
b = 83.17	β = 94.03
c = 163.652	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-02-27 
• Released Date: 2015-06-03 
Deposition Author(s): Dzurova, L., Savino, S., Forneris, F.

Revision History 

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2015-08-05
  Changes: Database references
• Version 2.0: 2019-06-26
  Changes: Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Other, Structure summary