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An HD-GYP cyclic di-guanosine monophosphate phosphodiesterase with a non-heme diiron-carboxylate active site. 2013

Kyle D Miner, and Karl E Klose, and Donald M Kurtz
Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA.

The intracellular level of the ubiquitous bacterial secondary messenger, cyclic di-(3',5')-guanosine monophosphate (c-di-GMP), represents a balance between its biosynthesis and degradation, the latter via specific phosphodiesterases (PDEs). One class of c-di-GMP PDEs contains a characteristic HD-GYP domain. Here we report that an HD-GYP PDE from Vibrio cholerae contains a non-heme diiron-carboxylate active site, and that only the reduced form is active. An engineered D-to-A substitution in the HD dyad caused loss of c-di-GMP PDE activity and of two iron atoms. This report constitutes the first demonstration that a non-heme diiron-carboxylate active site can catalyze the c-di-GMP PDE reaction and that this activity can be redox regulated in the HD-GYP class.

UI MeSH Term Description Entries
D007501 Iron A metallic element with atomic symbol Fe, atomic number 26, and atomic weight 55.85. It is an essential constituent of HEMOGLOBINS; CYTOCHROMES; and IRON-BINDING PROTEINS. It plays a role in cellular redox reactions and in the transport of OXYGEN. Iron-56,Iron 56
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D006152 Cyclic GMP Guanosine cyclic 3',5'-(hydrogen phosphate). A guanine nucleotide containing one phosphate group which is esterified to the sugar moiety in both the 3'- and 5'-positions. It is a cellular regulatory agent and has been described as a second messenger. Its levels increase in response to a variety of hormones, including acetylcholine, insulin, and oxytocin and it has been found to activate specific protein kinases. (From Merck Index, 11th ed) Guanosine Cyclic 3',5'-Monophosphate,Guanosine Cyclic 3,5 Monophosphate,Guanosine Cyclic Monophosphate,Guanosine Cyclic-3',5'-Monophosphate,3',5'-Monophosphate, Guanosine Cyclic,Cyclic 3',5'-Monophosphate, Guanosine,Cyclic Monophosphate, Guanosine,Cyclic-3',5'-Monophosphate, Guanosine,GMP, Cyclic,Guanosine Cyclic 3',5' Monophosphate,Monophosphate, Guanosine Cyclic
D006418 Heme The color-furnishing portion of hemoglobin. It is found free in tissues and as the prosthetic group in many hemeproteins. Ferroprotoporphyrin,Protoheme,Haem,Heme b,Protoheme IX
D001426 Bacterial Proteins Proteins found in any species of bacterium. Bacterial Gene Products,Bacterial Gene Proteins,Gene Products, Bacterial,Bacterial Gene Product,Bacterial Gene Protein,Bacterial Protein,Gene Product, Bacterial,Gene Protein, Bacterial,Gene Proteins, Bacterial,Protein, Bacterial,Proteins, Bacterial
D014734 Vibrio cholerae The etiologic agent of CHOLERA. Bacillus cholerae,Bacillus cholerae-asiaticae,Liquidivibrio cholerae,Microspira comma,Pacinia cholerae-asiaticae,Spirillum cholerae,Spirillum cholerae-asiaticae,Vibrio albensis,Vibrio cholera,Vibrio cholerae-asiaticae,Vibrio comma
D015106 3',5'-Cyclic-GMP Phosphodiesterases Enzymes that catalyze the hydrolysis of cyclic GMP to yield guanosine-5'-phosphate. 3',5'-Cyclic GMP 5'-Nucleotidohydrolase,3',5'-Cyclic GMP Phosphodiesterase,3',5'-Cyclic-GMP Phosphodiesterase,3,5-Cyclic GMP 5-Nucleotidohydrolase,3,5-Cyclic GMP Phosphodiesterase,3',5' Cyclic GMP 5' Nucleotidohydrolase,3',5' Cyclic GMP Phosphodiesterase,3',5' Cyclic GMP Phosphodiesterases,3,5 Cyclic GMP 5 Nucleotidohydrolase,3,5 Cyclic GMP Phosphodiesterase,5'-Nucleotidohydrolase, 3',5'-Cyclic GMP,5-Nucleotidohydrolase, 3,5-Cyclic GMP,GMP 5'-Nucleotidohydrolase, 3',5'-Cyclic,GMP 5-Nucleotidohydrolase, 3,5-Cyclic,GMP Phosphodiesterase, 3',5'-Cyclic,GMP Phosphodiesterase, 3,5-Cyclic,Phosphodiesterase, 3',5'-Cyclic GMP,Phosphodiesterase, 3',5'-Cyclic-GMP,Phosphodiesterase, 3,5-Cyclic GMP,Phosphodiesterases, 3',5'-Cyclic-GMP
D017434 Protein Structure, Tertiary The level of protein structure in which combinations of secondary protein structures (ALPHA HELICES; BETA SHEETS; loop regions, and AMINO ACID MOTIFS) pack together to form folded shapes. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Tertiary Protein Structure,Protein Structures, Tertiary,Tertiary Protein Structures
D020134 Catalytic Domain The region of an enzyme that interacts with its substrate to cause the enzymatic reaction. Active Site,Catalytic Core,Catalytic Region,Catalytic Site,Catalytic Subunit,Reactive Site,Active Sites,Catalytic Cores,Catalytic Domains,Catalytic Regions,Catalytic Sites,Catalytic Subunits,Core, Catalytic,Cores, Catalytic,Domain, Catalytic,Domains, Catalytic,Reactive Sites,Region, Catalytic,Regions, Catalytic,Site, Active,Site, Catalytic,Site, Reactive,Sites, Active,Sites, Catalytic,Sites, Reactive,Subunit, Catalytic,Subunits, Catalytic

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