4R8Z

Crystal Structure of PA4781 HD-GYP domain from Pseudomonas aeruginosa at 2.2A resolution showing a bi-metallic Ni ion center

Summary for 4R8Z

• Entry DOI: 10.2210/pdb4r8z/pdb
• Descriptor: Cyclic di-GMP phosphodiesterase, NICKEL (II) ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: bimetallic, c-di-gmp, pde, phosphdiesterase, cyclic-di-gmp, biofilm, hydrolase
• Biological source: Pseudomonas aeruginosa PAO1
• Total number of polymer chains: 2
• Total formula weight: 48321.89

Authors

Giardina, G.,Cutruzzolaa, F.,Rinaldo, S.,Stelitano, V. (deposition date: 2014-09-03, release date: 2015-03-04, Last modification date: 2024-02-28)

Primary citation

Rinaldo, S.,Paiardini, A.,Stelitano, V.,Brunotti, P.,Cervoni, L.,Fernicola, S.,Protano, C.,Vitali, M.,Cutruzzola, F.,Giardina, G.
Structural basis of functional diversification of the HD-GYP domain revealed by the Pseudomonas aeruginosa PA4781 protein, which displays an unselective bimetallic binding site.
J.Bacteriol., 197:1525-1535, 2015

PubMed Abstract: The intracellular level of the bacterial secondary messenger cyclic di-3',5'-GMP (c-di-GMP) is determined by a balance between its biosynthesis and degradation, the latter achieved via dedicated phosphodiesterases (PDEs) bearing a characteristic EAL or HD-GYP domain. We here report the crystal structure of PA4781, one of the three Pseudomonas aeruginosa HD-GYP proteins, which we have previously characterized in vitro. The structure shows a bimetallic active site whose metal binding mode is different from those of both HD-GYP PDEs characterized so far. Purified PA4781 does not contain iron in the active site as for other HD-GYPs, and we show that it binds to a wide range of transition metals with similar affinities. Moreover, the structural features of PA4781 indicate that this is preferentially a pGpG binding protein, as we previously suggested. Our results point out that the structural features of HD-GYPs are more complex than predicted so far and identify the HD-GYP domain as a conserved scaffold which has evolved to preferentially interact with a partner GGDEF but which harbors different functions obtained through diversification of the active site.

PubMed: 25691523
DOI: 10.1128/JB.02606-14

Experimental method

X-RAY DIFFRACTION (2.2 Å)