9ITF | pdb_00009itf

Cryo-EM structure of full-length phyB(Y276H)-PIF6beta complex

External Resource: Annotation


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth C]PHY, PAS, GAF, PAS_2e9itfC1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: PHY, PAS, GAF, PAS_2ECOD (v295.2)
A [auth C]ADP_ribosyl_GHe9itfC2 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: ADP_ribosyl_GHECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth C],
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
A [auth C],
B [auth A]		PF00360Phytochrome region (PHY)Phytochrome regionPhytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarit ...Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to Pfam:PF01590 [1], which is generally located immediately N-terminal to this domain. Compared with Pfam:PF01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilise the photoactivated far-red-absorbing state (Pfr) [1]. The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue [1].
Domain
A [auth C],
B [auth A]		PF08446PAS fold (PAS_2)PAS foldThe PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
C [auth B]Transcription factor PIF6
A [auth C],
B [auth A]		Phytochrome B

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
C [auth B]IPR047265Transcription factor PIF1-like, basic helix-loop-helix domainDomain
C [auth B]IPR011598Myc-type, basic helix-loop-helix (bHLH) domainDomain
C [auth B]IPR044273Transcription factor PIF3-likeFamily
C [auth B]IPR036638Helix-loop-helix DNA-binding domain superfamilyHomologous Superfamily
A [auth C],
B [auth A]		IPR012129Phytochrome A/B/C/D/EFamily
A [auth C],
B [auth A]		IPR003594Histidine kinase/HSP90-like ATPase domainDomain
A [auth C],
B [auth A]		IPR001294PhytochromeFamily
A [auth C],
B [auth A]		IPR035965PAS domain superfamilyHomologous Superfamily
A [auth C],
B [auth A]		IPR013515Phytochrome specific domainDomain
A [auth C],
B [auth A]		IPR005467Histidine kinase domainDomain
A [auth C],
B [auth A]		IPR029016GAF-like domain superfamilyHomologous Superfamily
A [auth C],
B [auth A]		IPR036890Histidine kinase/HSP90-like ATPase superfamilyHomologous Superfamily
A [auth C],
B [auth A]		IPR003661Signal transduction histidine kinase, dimerisation/phosphoacceptor domainDomain
A [auth C],
B [auth A]		IPR013654PAS fold-2Domain
A [auth C],
B [auth A]		IPR013516Phytochrome chromophore binding siteBinding Site
A [auth C],
B [auth A]		IPR003018GAF domainDomain
A [auth C],
B [auth A]		IPR016132Phytochrome chromophore attachment domainDomain
A [auth C],
B [auth A]		IPR013767PAS foldDomain
A [auth C],
B [auth A]		IPR044767Phytochrome A/B/C/D/E-like, histidine-kinase-related domainDomain
A [auth C],
B [auth A]		IPR000014PAS domainDomain
A [auth C],
B [auth A]		IPR043150Phytochrome, PHY domain superfamilyHomologous Superfamily