SMART: PAC domain annotation

PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)

SMART accession number:	SM00086
Description:	PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Interpro abstract (IPR001610):	PAC motifs occur C-terminal to a subset of all known PAS motifs (see IPR000014). It is proposed to contribute to the PAS domain fold [(PUBMED:9301332), (PUBMED:7756254), (PUBMED:9382818)].
GO process:	signal transduction (GO:0007165), regulation of transcription, DNA-dependent (GO:0006355)
Family alignment:	View or

There are 27735 PAC domains in 17805 proteins in SMART's nrdb database.

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Evolution (species in which this domain is found)
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This tree shows only several representative species. The complete taxonomic breakdown of all proteins with PAC domain is also avaliable.

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Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Takifugu rubripes
Literature (relevant references for this domain)
Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Pellequer JL, Wager-Smith KA, Kay SA, Getzoff ED
- Photoactive yellow protein: a structural prototype for the three-dimensional fold of the PAS domain superfamily.
- Proc Natl Acad Sci U S A. 1998; 95: 5884-90
- Display abstract
- PAS domains are found in diverse proteins throughout all three kingdoms of life, where they apparently function in sensing and signal transduction. Although a wealth of useful sequence and functional information has become recently available, these data have not been integrated into a three-dimensional (3D) framework. The very early evolutionary development and diverse functions of PAS domains have made sequence analysis and modeling of this protein superfamily challenging. Limited sequence similarities between the approximately 50-residue PAS repeats and one region of the bacterial blue-light photosensor photoactive yellow protein (PYP), for which ground-state and light-activated crystallographic structures have been determined to high resolution, originally were identified in sequence searches using consensus sequence probes from PAS-containing proteins. Here, we found that by changing a few residues particular to PYP function, the modified PYP sequence probe also could select PAS protein sequences. By mapping a typical approximately 150-residue PAS domain sequence onto the entire crystallographic structure of PYP, we show that the PAS sequence similarities and differences are consistent with a shared 3D fold (the PAS/PYP module) with obvious potential for a ligand-binding cavity. Thus, PYP appears to prototypically exhibit all the major structural and functional features characteristic of the PAS domain superfamily: the shared PAS/PYP modular domain fold of approximately 125-150 residues, a sensor function often linked to ligand or cofactor (chromophore) binding, and signal transduction capability governed by heterodimeric assembly (to the downstream partner of PYP). This 3D PAS/PYP module provides a structural model to guide experimental testing of hypotheses regarding ligand-binding, dimerization, and signal transduction.
- Rutila JE, Suri V, Le M, So WV, Rosbash M, Hall JC
- CYCLE is a second bHLH-PAS clock protein essential for circadian rhythmicity and transcription of Drosophila period and timeless.
- Cell. 1998; 93: 805-14
- Display abstract
- We report the identification, characterization, and cloning of another novel Drosophila clock gene, cycle (cyc). Homozygous cyc flies are completely arrhythmic. Heterozygous cyc/+ flies are rhythmic but have altered periods, indicating that the cyc locus has a dosage effect on period. The molecular circadian phenotype of homozygous cyc flies is like homozygous Clk flies presented in the accompanying paper: mutant flies have little or no transcription of the per and tim genes. Cloning of the gene indicates that it also encodes a bHLH-PAS transcription factor and is a Drosophila homolog of the human protein BMAL1. cyc is a nonsense mutation, consistent with its strong loss-of-function phenotype. We propose that the CYC:CLK heterodimer binds to per and tim E boxes and makes a major contribution to the circadian transcription of Drosophila clock genes.
- Ponting CP, Aravind L
- PAS: a multifunctional domain family comes to light.
- Curr Biol. 1997; 7: 6747-6747
- Zelzer E, Wappner P, Shilo BZ
- The PAS domain confers target gene specificity of Drosophila bHLH/PAS proteins.
- Genes Dev. 1997; 11: 2079-89
- Display abstract
- Trachealess (Trh) and Single-minded (Sim) are highly similar Drosophila bHLH/PAS transcription factors. They activate nonoverlapping target genes and induce diverse cell fates. A single Drosophila gene encoding a bHLH/PAS protein homologous to the vertebrate ARNT protein was isolated and may serve as a partner for both Trh and Sim. We show that Trh and Sim complexes recognize similar DNA-binding sites in the embryo. To examine the basis for their distinct target gene specificity, the activity of Trh-Sim chimeric proteins was monitored in embryos. Replacement of the Trh PAS domain by the analogous region of Sim was sufficient to convert it into a functional Sim protein. The PAS domain thus mediates all the features conferring specificity and the distinct recognition of target genes. The normal expression pattern of additional proteins essential for the activity of the Trh or Sim complexes can be inferred from the induction pattern of target genes and binding-site reporters, triggered by ubiquitous expression of Trh or Sim. We postulate that the capacity of bHLH/PAS heterodimers to associate, through the PAS domain, with additional distinct proteins that bind target-gene DNA, is essential to confer specificity.
- Zhulin IB, Taylor BL, Dixon R
- PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox.
- Trends Biochem Sci. 1997; 22: 331-3
- Borgstahl GE, Williams DR, Getzoff ED
- 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore.
- Biochemistry. 1995; 34: 6278-87
- Display abstract
- A photosensing protein directs light energy captured by its chromophore into a photocycle. The protein's structure must accommodate the photocycle and promote the resulting chemical or conformational changes that lead to signal transduction. The 1.4 A crystallographic structure of photoactive yellow protein, determined by multiple isomorphous replacement methods, provides the first view at atomic resolution of a protein with a photocycle. The alpha/beta fold, which differs from the original chain tracing, shows striking similarity to distinct parts of the signal transduction proteins profilin and the SH2 domain. In the dark state structure of photoactive yellow protein, the novel 4-hydroxycinnamyl chromophore, covalently attached to Cys69, is buried within the major hydrophobic core of the protein and is tethered at both ends by hydrogen bonds. In the active site, the yellow anionic form of the chromophore is stabilized by hydrogen bonds from the side chains of Tyr42 and buried Glu46 to the phenolic oxygen atom and by electrostatic complementarity with the positively charged guanidinium group of Arg52. Thr50 further interlocks Tyr42, Glu46, and Arg52 through a network of active site hydrogen bonds. Arg52, located in a concavity of the protein surface adjacent to the dominant patch of negative electrostatic potential, shields the chromophore from solvent and is positioned to form a gateway for the phototactic signal. Overall, the high-resolution structure of photoactive yellow protein supports a mechanism whereby electrostatic interactions create an active site poised for photon-induced rearrangements and efficient protein-mediated signal transduction.
Metabolism (metabolic pathways involving proteins which contain this domain)

Structure (3D structures containing this domain)

3D Structures of PAC domains in PDB

PDB code	Main view	Title
1byw		Structure of the n-terminal domain of the human-erg potassium channel
1dp6		Oxygen-binding complex of fixl heme domain
1dp8		Crystal structure of the nitric oxide bound fixl heme domain
1dp9		Crystal structure of imidazole-bound fixl heme domain
1drm		Crystal structure of the ligand free bjfixl heme domain
1dwy		Bovine prion protein fragment 121-230
1dwz		Bovine prion protein fragment 121-230
1dx0		Bovine prion protein residues 23-230
1dx1		Bovine prion protein residues 23-230
1g28		Structure of a flavin-binding domain, lov2, from the chimeric phytochrome/phototropin photoreceptor phy3
1jnu		Photoexcited structure of the plant photoreceptor domain, phy3 lov2
1lsv		Crystal structure of the co-bound bjfixl heme domain
1lsw		Crystal structure of the ferrous bjfixl heme domain
1lsx		Crystal structure of the methylimidazole-bound bjfixl heme domain
1lt0		Crystal structure of the cn-bound bjfixl heme domain
1n9l		Crystal structure of the phot-lov1 domain from chlamydomonas reinhardtii in the dark state.
1n9n		Crystal structure of the phot-lov1 domain from chlamydomonas reinhardtii in illuminated state. data set of a single crystal.
1n9o		Crystal structure of the phot-lov1 domain from chlamydomonas reinhardtii in illuminated state. composite data set.
1p97		Nmr structure of the c-terminal pas domain of hif2a
1s66		Crystal structure of heme domain of direct oxygen sensor from e. coli
1s67		Crystal structure of heme domain of direct oxygen sensor from e. coli
1v9y		Crystal structure of the heme pas sensor domain of ec dos (ferric form)
1v9z		Crystal structure of the heme pas sensor domain of ec dos (ferrous form)
1vb6		Crystal structure of the heme pas sensor domain of ec dos (oxygen-bound form)
1wa9		Crystal structure of the pas repeat region of the drosophila clock protein period
1x0o		Human arnt c-terminal pas domain
1xj2		Co-bound structure of bjfixlh
1xj3		Bjfixlh in unliganded ferrous form
1xj4		Co-bound structure of bjfixlh
1xj6		Structure of bjfixlh in the unliganded ferrous form
1y28		Crystal structure of the r220a metbjfixl heme domain
2a24		Haddock structure of hif-2a/arnt pas-b heterodimer
2b02		Crystal structure of arnt pas-b domain
2cmn		A proximal arginine residue in the switching mechanism of the fixl oxygen sensor
2gj3		Crystal structure of the fad-containing pas domain of the protein nifl from azotobacter vinelandii.
2hv1		Haddock structure of arnt pas-b homodimer
2k7s		Human arnt c-terminal pas domain, 3 residue ib slip
2owh		Structure of an early-microsecond photolyzed state of co- bjfixlh
2owj		Structure of an early-microsecond photolyzed state of co- bjfixlh, dark state
2pd7		2.0 angstrom crystal structure of the fungal blue-light photoreceptor vivid
2pd8		1.8 angstrom crystal structure of the cys71ser mutant of vivid
2pdr		1.7 angstrom crystal structure of the photo-excited blue- light photoreceptor vivid
2pdt		2.3 angstrom structure of phosphodiesterase treated vivid
2pr5		Structural basis for light-dependent signaling in the dimeric lov photosensor ytva (dark structure)
2pr6		Structural basis for light-dependent signaling in the dimeric lov photosensor ytva (light structure)
2v0u		N- and c-terminal helices of oat lov2 (404-546) are involved in light-induced signal transduction (cryo dark structure of lov2 (404-546))
2v0w		N- and c-terminal helices of oat lov2 (404-546) are involved in light-induced signal transduction (cryo- trapped light structure of lov2 (404-546))
2v1a		N- and c-terminal helices of oat lov2 (404-546) are involved in light-induced signal transduction (room temperature (293k) dark structure of lov2 (404-546))
2v1b		N- and c-terminal helices of oat lov2 (404-546) are involved in light-induced signal transduction (room temperature (293k) light structure of lov2 (404-546))
2vlg		Kina pas-a domain, homodimer
2vv6		Bjfixlh in ferric form
2vv7		Bjfixlh in unliganded ferrous form
2vv8		Co-bound structure of bjfixlh
2wkp		Structure of a photoactivatable rac1 containing lov2 wildtype
2wkq		Structure of a photoactivatable rac1 containing the lov2 c450a mutant
2wkr		Structure of a photoactivatable rac1 containing the lov2 c450m mutant
2z6c		Crystal structure of lov1 domain of phototropin1 from arabidopsis thaliana
2z6d		Crystal structure of lov1 domain of phototropin2 from arabidopsis thaliana
3d72		1.65 angstrom crystal structure of the cys71val variant in the fungal photoreceptor vvd
3ewk		Structure of the redox sensor domain of methylococcus capsulatus (bath) mmos
3f1n		Crystal structure of a high affinity heterodimer of hif2 alpha and arnt c-terminal pas domains, with internally bound ethylene glycol.
3f1o		Crystal structure of the high affinity heterodimer of hif2 alpha and arnt c-terminal pas domains, with an internally- bound artificial ligand
3f1p		Crystal structure of a high affinity heterodimer of hif2 alpha and arnt c-terminal pas domains
3gdi		Mammalian clock protein mper2 - crystal struture of a pas domain fragment
3gec		Crystal structure of a tandem pas domain fragment of drosophila period
3h9w		Crystal structure of the n-terminal domain of diguanylate cyclase with pas/pac sensor (maqu_2914) from marinobacter aquaeolei, northeast structural genomics consortium target mqr66c
3hji		1.8 angstrom crystal structure of the i74v:i85v variant of vivid (vvd).
3hjk		2.0 angstrom structure of the ile74val variant of vivid (vvd).
3is2		2.3 angstrom crystal structure of a cys71 sulfenic acid form of vivid

Links (links to other resources describing this domain)
INTERPRO IPR001610