3EK5

Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Unique GTP-Binding Pocket and Allostery of Uridylate Kinase from a Gram-Negative Phytopathogenic Bacterium

Tu, J.-L.Chin, K.-H.Wang, A.H.-J.Chou, S.-H.

(2009) J Mol Biol 385: 1113-1126

  • DOI: https://doi.org/10.1016/j.jmb.2008.11.030
  • Primary Citation of Related Structures:  
    3EK5, 3EK6

  • PubMed Abstract: 

    Using X-ray diffraction methodology, we have successfully determined the tertiary structures of the apo- and GTP-bound forms of uridylate kinase (UMPK) from the gram-negative plant pathogen Xanthomonas campestris with crystals grown under a strong magnetic field. The flexible ATP- and UMP-binding loops are clearly shown under this situation. X. campestris UMPK contains a unique patch of noticeably positive nature from residue R100 to residue R127, allowing it to form a special GTP-binding pocket in the central hole of the structure. Although GTP is found to be situated in a pocket similar to that of the ATP-binding pocket in Bacillus anthracis UMPK, superimposition between the two pockets indicates that they adopt very distinct conformations. Detailed structural analyses of X. campestris UMPK between its apo- and GTP-bound forms reveal that binding of GTP does not induce global conformational change for X. campestris UMPK and only moderates movements for the ATP- and UMP-binding loops. Binding of GTP effector seems to "heat up" X. campestris UMPK, causing overall increases of B-factors for the protein, except for residues interacting with the guanine base. Moderate increase of enzyme activity, as is the case detected in other gram-negative bacteria, is observed for X. campestris UMPK in the presence of an allosteric GTP effector. Given that the GTP molecules bind in the central cavity of the hexamer and that each GTP molecule interacts with more than one monomer, it is likely that binding of GTP modifies the hexameric assembly to exert long-range allosteric control on X. campestris UMPK, similar to that suggested for the effect of ATP effector on B. anthracis UMPK.


  • Organizational Affiliation

    Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridylate kinase
A, B, C, D, E
A, B, C, D, E, F
243Xanthomonas campestris pv. campestrisMutation(s): 0 
Gene Names: pyrHXCC1371
EC: 2.7.4.22
UniProt
Find proteins for P59009 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25))
Explore P59009 
Go to UniProtKB:  P59009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59009
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.634α = 90
b = 119.638β = 90
c = 125.18γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
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: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description