Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains.
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.
Minasov
George
G
Department of Molecular Pharmacology and Biological Chemistry and Midwest Center for Structural Genomics, Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA.
Padavattan
Sivaraman
S
Shuvalova
Ludmilla
L
Brunzelle
Joseph S
JS
Miller
Darcie J
DJ
Baslé
Arnaud
A
Massa
Claudia
C
Collart
Frank R
FR
Schirmer
Tilman
T
Anderson
Wayne F
WF
D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D002384:Catalysis; D003460:Crystallization; D018360:Crystallography, X-Ray; D006152:Cyclic GMP / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D010755:Organophosphates / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D015290:Second Messenger Systems; D012645:Selenomethionine; D017386:Sequence Homology, Amino Acid
D001426:Bacterial Proteins; D010755:Organophosphates; C062025:bis(3',5')-cyclic diguanylic acid; D012645:Selenomethionine; D006152:Cyclic GMP