2W27

CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS YKUI PROTEIN, WITH AN EAL DOMAIN, IN COMPLEX WITH SUBSTRATE C-DI-GMP AND CALCIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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This is version 1.4 of the entry. See complete history


Literature

Crystal Structures of Ykui and its Complex with Second Messenger C-Di-Gmp Suggests Catalytic Mechanism of Phosphodiester Bond Cleavage by Eal Domains.

Minasov, G.Padavattan, S.Shuvalova, L.Brunzelle, J.S.Miller, D.J.Basle, A.Massa, C.Collart, F.R.Schirmer, T.Anderson, W.F.

(2009) J Biol Chem 284: 13174

  • DOI: https://doi.org/10.1074/jbc.M808221200
  • Primary Citation of Related Structures:  
    2BAS, 2W27

  • PubMed Abstract: 

    Cyclic di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that is involved in the regulation of cell surface-associated traits and the persistence of infections. Omnipresent GGDEF and EAL domains, which occur in various combinations with regulatory domains, catalyze c-di-GMP synthesis and degradation, respectively. The crystal structure of full-length YkuI from Bacillus subtilis, composed of an EAL domain and a C-terminal PAS-like domain, has been determined in its native form and in complex with c-di-GMP and Ca(2+). The EAL domain exhibits a triose-phosphate isomerase-barrel fold with one antiparallel beta-strand. The complex with c-di-GMP-Ca(2+) defines the active site of the putative phosphodiesterase located at the C-terminal end of the beta-barrel. The EAL motif is part of the active site with Glu-33 of the motif being involved in cation coordination. The structure of the complex allows the proposal of a phosphodiesterase mechanism, in which the divalent cation and the general base Glu-209 activate a catalytic water molecule for nucleophilic in-line attack on the phosphorus. The C-terminal domain closely resembles the PAS-fold. Its pocket-like structure could accommodate a yet unknown ligand. YkuI forms a tight dimer via EAL-EAL and trans EAL-PAS-like domain association. The possible regulatory significance of the EAL-EAL interface and a mechanism for signal transduction between sensory and catalytic domains of c-di-GMP-specific phosphodiesterases are discussed.


  • Organizational Affiliation

    Department of Molecular Pharmacology and Biological Chemistry and Midwest Center for Structural Genomics, Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YKUI PROTEIN
A, B
431Bacillus subtilisMutation(s): 0 
UniProt
Find proteins for O35014 (Bacillus subtilis (strain 168))
Explore O35014 
Go to UniProtKB:  O35014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35014
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.167α = 90
b = 124.521β = 90
c = 168.751γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2019-01-30
    Changes: Advisory, Data collection, Experimental preparation
  • Version 1.3: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description