Putative sugar kinases from Synechococcus elongatus PCC7942 in complex with AMPPNP

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 

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Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana

Xie, Y.Li, M.Chang, W.

(2016) PLoS One 11: e0156067-e0156067

  • DOI: https://doi.org/10.1371/journal.pone.0156067
  • Primary Citation of Related Structures:  
    5HTJ, 5HTN, 5HTP, 5HTR, 5HTV, 5HTX, 5HTY, 5HU2, 5HUX, 5HV7

  • PubMed Abstract: 

    The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. Sequence alignment suggests that both kinases belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. However, their exact physiological function and real substrates remain unknown. Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. The two kinases exhibit nearly identical overall architecture, with both kinases possessing ATP hydrolysis activity in the absence of substrates. In addition, our enzymatic assays suggested that SePSK has the capability to phosphorylate D-ribulose. In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. Using mutation and activity analysis, we further verified the key residues important for its catalytic activity. Moreover, our structural comparison with other family members suggests that there are major conformational changes in SePSK upon substrate binding, facilitating the catalytic process. Together, these results provide important information for a more detailed understanding of the cofactor and substrate binding mode as well as the catalytic mechanism of SePSK, and possible similarities with its plant homologue AtXK-1.

  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable sugar kinase436Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: Synpcc7942_2462
Find proteins for Q31KC7 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31KC7 
Go to UniProtKB:  Q31KC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31KC7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ANP

Download Ideal Coordinates CCD File 
C10 H17 N6 O12 P3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.515α = 90
b = 46.567β = 91
c = 87.991γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations