5ITS

Crystal structure of LOG from Corynebacterium glutamicum

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for cytokinin production by LOG from Corynebacterium glutamicum

Seo, H.-G., Kim, S., Sagong, H.Y., Son, H.F., Jin, K.S., Kim, I.K., Kim, K.J.

(2016) Sci Rep 6: 31390-31390

  • DOI: 10.1038/srep31390
  • Primary Citation of Related Structures:  
    5ITS

  • PubMed Abstract: 

    • "Lonely guy" (LOG) has been identified as a cytokinin-producing enzyme in plants and plant-interacting fungi. The gene product of Cg2612 from the soil-dwelling bacterium Corynebacterium glutamicum was annotated as an LDC. However, the facts that C. glutamicum lacks an LDC and Cg2612 has high amino acid similarity with LOG proteins suggest that Cg2612 is possibly an LOG protein ...

    "Lonely guy" (LOG) has been identified as a cytokinin-producing enzyme in plants and plant-interacting fungi. The gene product of Cg2612 from the soil-dwelling bacterium Corynebacterium glutamicum was annotated as an LDC. However, the facts that C. glutamicum lacks an LDC and Cg2612 has high amino acid similarity with LOG proteins suggest that Cg2612 is possibly an LOG protein. To investigate the function of Cg2612, we determined its crystal structure at a resolution of 2.3 Å. Cg2612 functions as a dimer and shows an overall structure similar to other known LOGs, such as LOGs from Arabidopsis thaliana (AtLOG), Claviceps purpurea (CpLOG), and Mycobacterium marinum (MmLOG). Cg2612 also contains a "PGGXGTXXE" motif that contributes to the formation of an active site similar to other LOGs. Moreover, biochemical studies on Cg2612 revealed that the protein has phosphoribohydrolase activity but not LDC activity. Based on these structural and biochemical studies, we propose that Cg2612 is not an LDC family enzyme, but instead belongs to the LOG family. In addition, the prenyl-binding site of Cg2612 (CgLOG) comprised residues identical to those seen in AtLOG and CpLOG, albeit dissimilar to those in MmLOG. The work provides structural and functional implications for LOG-like proteins from other microorganisms.

    Organizational Affiliation: 

    School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701, Republic of Korea.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytokinin riboside 5'-monophosphate phosphoribohydrolaseA, B, C, D203Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl2379
EC: 3.2.2
UniProt
Find proteins for Q8NN34 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore Q8NN34 
Go to UniProtKB:  Q8NN34
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NN34
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.506α = 90
b = 130.501β = 90
c = 140.512γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data processing
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2016-03-17 
  • Released Date: 2016-08-24 
    • Deposition Author(s): Seo, H.-G., Kim, K.-J.

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Derived calculations, Structure summary