Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 103.04 kDa 
• Atom Count: 6735 
• Modelled Residue Count: 796 
• Deposited Residue Count: 862 
• Unique protein chains: 1

2W27

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

• DOI: 10.2210/pdb2W27/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-10-24 Released: 2009-02-24 
• Deposition Author(s): Padavattan, S., AndERSON, W.F., Schirmer, T.

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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 

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

• PubMed: 19244251 
• DOI: 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YKUI PROTEIN	A, B	431	Bacillus subtilis	Mutation(s): 0
Find proteins for O35014 (Bacillus subtilis (strain 168)) Explore O35014  Go to UniProtKB:  O35014

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	A, B	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 46.167	α = 90
b = 124.521	β = 90
c = 168.751	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-10-24 
• Released Date: 2009-02-24 
Deposition Author(s): Padavattan, S., AndERSON, W.F., Schirmer, T.

Revision History  

• 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