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Literature summary for 3.1.4.52 extracted from

  • Bellini, D.; Caly, D.L.; McCarthy, Y.; Bumann, M.; An, S.Q.; Dow, J.M.; Ryan, R.P.; Walsh, M.A.
    Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre (2014), Mol. Microbiol., 91, 26-38.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.1.4.52

Cloned(Commentary)

Cloned (Comment) Organism
gene perma_0986, expression of N-terminally His6-tagged enzyme in Escherichiia coli strain BL21 (DE3) Persephonella marina

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant detagged enzyme in complex with Fe2+, substrate cyclic di-3',5'-guanylate or final product GMP, hanging drop vapour diffusion method, mixing of equal volumes of 10 mg/ml protein with a precipitant solution made up of 0.1 M MES pH 6.5, 0.9 M succinic acid, and 2% PEG 2000, anomalous X-ray diffraction structure determination and analysis at 2.03-2.8 A resolution Persephonella marina

Protein Variants

Protein Variants Comment Organism
D183A site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme Persephonella marina
D222A site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme Persephonella marina
D305A site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme Persephonella marina
E185A site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme Persephonella marina
G284A site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme Persephonella marina
H189A site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme Persephonella marina
H221A site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme Persephonella marina
H250A site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme Persephonella marina
H276A site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme Persephonella marina
H277A site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme Persephonella marina
K225A site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme Persephonella marina
K317A site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme Persephonella marina
P286A site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme Persephonella marina
R314 A site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme Persephonella marina
Y285 A site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme Persephonella marina

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ trinuclear Fe binding site located at the bottom of the HD-GYP domain cavity formed by the two claws of the open chela. Residues E185, H189, H221, D222, H250, H276, H277, and D305 are involved in metal binding Persephonella marina
Mg2+ required for catalysis Persephonella marina
Mn2+ required for catalysis Persephonella marina

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
cyclic di-3',5'-guanylate + H2O Persephonella marina
-
 5'-phosphoguanylyl(3'->5')guanosine final product is GMP ?
cyclic di-3',5'-guanylate + H2O Persephonella marina EX-H1
-
 5'-phosphoguanylyl(3'->5')guanosine final product is GMP ?

Organism

Organism UniProt Comment Textmining
Persephonella marina
-
 gene perma_0986
-
Persephonella marina EX-H1
-
 gene perma_0986
-

Purification (Commentary)

Purification (Comment) Organism
recombinant N-terminally His6-tagged enzyme from Escherichiia coli strain BL21(DE3) by nickel affinity chromatography and cleavage of the the His-tag by HRV 3C protease Persephonella marina

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
cyclic di-3',5'-guanylate + H2O
-
 Persephonella marina 5'-phosphoguanylyl(3'->5')guanosine final product is GMP ?
cyclic di-3',5'-guanylate + H2O
-
 Persephonella marina EX-H1 5'-phosphoguanylyl(3'->5')guanosine final product is GMP ?
additional information substrate and product binding structures, overview Persephonella marina ?
-
 ?
additional information substrate and product binding structures, overview Persephonella marina EX-H1 ?
-
 ?

Subunits

Subunits Comment Organism
dimer the enzyme forms a dimer with each monomer consisting of an N-terminal GAF domain connected to a C-terminal HD-GYP domain by an approximately 42 residue-long helix. Assembly of the head-to-head dimer relies exclusively on the GAF domain and the long alpha5 helix with the HD-GYP domain playing no role in the dimeric interface, crstal structure analysis, overview Persephonella marina
More primary sequence and three-dimensional structure comparisons, overview Persephonella marina

Synonyms

Synonyms Comment Organism
GAF/HD-GYP protein
-
 Persephonella marina
HD-GYP domain cyclic-di-GMP phosphodiesterase
-
 Persephonella marina
HD-GYP phosphodiesterase
-
 Persephonella marina
perma_0986
-
 Persephonella marina
PmGH
-
 Persephonella marina

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
 assay at Persephonella marina

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.6
-
 assay at Persephonella marina

General Information

General Information Comment Organism
additional information the enzyme comprises a HD-GYP domain fused to a GAF domain. D183 and K225 are catalytic residues, GYP domain residues R314, K317, G284, Y285 and P286 are involved in substrate binding, substrate and product binding structures, overview Persephonella marina