6MZB | pdb_00006mzb

Cryo-EM structure of phosphodiesterase 6


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth B]PDEase_Ie6mzbB1 A: alpha complex topologyX: PDEase-likeH: HD-domain/PDEase-like (From Topology)T: HD-domain/PDEase-likeF: PDEase_IECOD (1.6)
A [auth B]GAFe6mzbB2 A: a+b three layersX: Profilin-likeH: sensor domains (From Topology)T: sensor domainsF: GAFECOD (1.6)
CPDE6_gammae6mzbC1 A: extended segmentsX: cGMP phosphodiesterase gamma subunit (From Topology)H: cGMP phosphodiesterase gamma subunit (From Topology)T: cGMP phosphodiesterase gamma subunitF: PDE6_gammaECOD (1.6)
DPDE6_gammae6mzbD1 A: extended segmentsX: cGMP phosphodiesterase gamma subunit (From Topology)H: cGMP phosphodiesterase gamma subunit (From Topology)T: cGMP phosphodiesterase gamma subunitF: PDE6_gammaECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth B]PF01590GAF domain (GAF)GAF domainThis domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regul ...This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Domain
A [auth B]PF002333'5'-cyclic nucleotide phosphodiesterase (PDEase_I)3'5'-cyclic nucleotide phosphodiesteraseDomain
B [auth A]PF01590GAF domain (GAF)GAF domainThis domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regul ...This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Domain
B [auth A]PF002333'5'-cyclic nucleotide phosphodiesterase (PDEase_I)3'5'-cyclic nucleotide phosphodiesteraseDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth B]Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
B [auth A]Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha
C, D
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma