Catalyzes the hydrolysis of the 3'-5' phosphodiester bond of glycerophosphodiesters such as glycerophosphorylethanolamine (GPE), a typical phospholipid metabolite which is probably the natural substrate of the enzyme (PubMed:14711669). In addition, exhibits a broad substrate specificity and can catalyze the hydrolysis of various phosphomonoesters, diesters, triesters and phosphothiolates (PubMed:14711669, PubMed:168197, PubMed:17630782). Preferentially hydrolyzes the phosphate diesters over the phosphonate monoesters (PubMed:17630782). Can hydrolyze the model substrates p-nitrophenyl phosphate (pNPP), bis-(p-nitrophenyl phosphate) (bis(pNPP)) and ethyl p-nitrophenyl phosphate (EtpNPP) (PubMed:168197, PubMed:14711669, PubMed:17306828, PubMed:17630782, PubMed:18678932, PubMed:18831553). Also exhibits activity towards some organophosphate pesticides and is capable of hydrolyzing a close analog of EA 2192, the most toxic and persistent degradation product of the nerve agent VX (PubMed:14711669, PubMed:17630782). a sn-glycero-3-phosphodiester + H2O = an alcohol + H(+) + sn-glycerol 3-phosphate H2O + sn-glycero-3-phosphoethanolamine = ethanolamine + H(+) + sn-glycerol 3-phosphate Binds 2 Fe(2+) ions per subunit (PubMed:18678932). Active in the presence of various divalent cations such as Fe(2+), Zn(2+), Cd(2+), Co(2+) and Mn(2+) (PubMed:17306828, PubMed:17630782, PubMed:18535849, PubMed:18678932, PubMed:18831553). Fe(2+) is probably the native metal ion (PubMed:18678932). The active site contains a binuclear metal center, with a fully occupied alpha-metal ion site, and partially occupied beta-metal ion site (PubMed:17306828, PubMed:18678932, PubMed:18831553). The presence of substrate promotes the formation of a catalytically competent binuclear center by significantly enhancing the binding affinity of one of the metal ions in the active site (PubMed:18831553). kcat is 2.78 sec(-1) with bis(pNPP) as substrate (in the presence of Fe(2+)) (PubMed:18678932). kcat is 0.176 sec(-1) with bis(pNPP) as substrate (in the presence of Zn(2+)) (PubMed:18678932). kcat is 0.107 sec(-1) with bis(pNPP) as substrate (in the presence of Zn(2+)) (PubMed:17306828). kcat is 1.62 sec(-1) with bis(pNPP) as substrate (in the presence of Co(2+)) (PubMed:17306828). kcat is 1.89 sec(-1) with bis(pNPP) as substrate (in the presence of Co(2+)) (PubMed:18831553). kcat is 15 sec(-1) with bis(pNPP) as substrate (in the presence of Cd(2+)) (PubMed:18535849). Optimum pH is 5.0 for mono- and diesters hydrolysis. Homohexamer (PubMed:168197, PubMed:17306828, PubMed:18831553). Trimer of dimers (PubMed:17306828). Tends to form a dimer under crystallization conditions (PubMed:16820687). Induced under phosphate-limiting conditions. Deletion mutant is unable to grow by using dimethyl phosphate (DMP) or the phosphotriesters as phosphorus sources. Is of interest for its potential application as a bioremediator in the destruction of organophosphate pesticides and in the detoxification of nerve agents (PubMed:17630782, PubMed:18535849). The Ser127Ala mutant, which possesses improved metal binding abilities, has been immobilized on magnetite nanoparticles and shown to be active for multiple cycles, and could be stored over a prolonged time in the immobilized form without loss of activity. This system has the potential to be of potential use in the bioremediation of organophosphate contaminated waterways (PubMed:24239906). Diester bonds are cleaved in two separate (non-processive) reactions, indicating that GpdQ may regenerate its active site after the first hydrolysis (PubMed:19923005). The metal ion-bridging hydroxide molecule activates a terminally bound hydroxide nucleophile (PubMed:20163105). Belongs to the cyclic nucleotide phosphodiesterase class-III family.