5AJU | pdb_00005aju

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

• PDB DOI: https://doi.org/10.2210/pdb5AJU/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: 2.50 Å
• R-Value Free: 
  0.243 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

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

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


• 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.
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.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 29.5 kDa 
• Atom Count: 1,668 
• Modeled Residue Count: 217 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOHYDROLASE LONELY GUY	A	274	Claviceps purpurea	Mutation(s): 0
UniProt
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
RP5	B [auth A]	5-O-phosphono-beta-D-ribofuranose C5 H11 O8 P KTVPXOYAKDPRHY-TXICZTDVSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.243 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.97	α = 90
b = 78.97	β = 90
c = 144.64	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary