SMART: PAS domain annotation

PAS PAS domain

SMART accession number:	SM00091
Description:	PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Interpro abstract (IPR000014):	PAS domains are involved in many signalling proteins where they are used as a signal sensor domain [(PUBMED:10357859)]. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs [(PUBMED:15009198)]. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand [(PUBMED:12377121)]. Probably the most surprising identification of a PAS domain was that in EAG-like K⁺-channels [(PUBMED:9301332)].
GO process:	signal transduction (GO:0007165)
GO function:	signal transducer activity (GO:0004871)
Family alignment:	View or

There are 44299 PAS domains in 29283 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 PAS 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, Saccharomyces cerevisiae, Takifugu rubripes
Literature (relevant references for this domain)
Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- 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 PAS domains in PDB

PDB code	Main view	Title
1d06		Structural basis of dimerization and sensory mechanisms of oxygen-sensing domain of rhizobium meliloti fixl determined at 1.4a resolution
1d7e		Crystal structure of the p65 crystal form of photoactive yellow protein
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
1ew0		Crystal structure analysis of the sensor domain of rmfixl(ferrous form)
1f98		Crystal structure of the photoactive yellow protein mutant t50v
1f9i		Crystal structure of the photoactive yellow protein mutant y42f
1gsv		Crystal structure of the p65 crystal form of photoactive yellow protein g47s mutant
1gsw		Crystal structure of the p65 crystal form of photoactive yellow protein g51s mutant
1gsx		Crystal structure of the p65 crystal form of photoactive yellow protein g47s/g51s mutant
1kou		Crystal structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 a resolution
1ll8		Structure and interactions of pas kinase n-terminal pas domain: model for intramolecular kinase regulation
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
1mzu		Crystal structure of the photoactive yellow protein domain from the sensor histidine kinase ppr from rhodospirillum centenum
1nwz		Pyp ultra-high resolution structure of a bacterial photoreceptor
1odv		Photoactive yellow protein 1-25 deletion mutant
1ot6		Cryotrapped crystal structure of the e46q mutant of photoactive yellow protein under continuous illumination at 110k
1ot9		Cryotrapped state in wild type photoactive yellow protein, induced with continuous illumination at 110k
1ota		E46q mutant of photoactive yellow protein, p63 at 295k
1otb		Wild type photoactive yellow protein, p63 at 295k
1otd		Strong hydrogen bonds in photoactive yellow protein and their role in its photocycle
1ote		E46q mutant of photoactive yellow protein, p65 at 110k
1oti		E46q mutant of photoactive yellow protein, p65 at 295k
1p97		Nmr structure of the c-terminal pas domain of hif2a
1s1y		Photoactivated chromophore conformation in photoactive yellow protein (e46q mutant) from 10 microseconds to 3 milliseconds
1s1z		Photoactivated chromophore conformation in photoactive yellow protein (e46q mutant) from 10 to 500 nanoseconds
1s4r		Structure of a reaction intermediate in the photocycle of pyp extracted by a svd-driven analysis
1s4s		Reaction intermediate in the photocycle of pyp, intermediate occupied between 100 micro-seconds to 5 milli- seconds
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
1t18		Early intermediate ie1 from time-resolved crystallography of the e46q mutant of pyp
1t19		Early intermediate ie2 from time-resolved crystallography of the e46q mutant of pyp
1t1a		Late intermediate il1 from time-resolved crystallography of the e46q mutant of pyp
1t1b		Late intermediate il2 from time-resolved crystallography of the e46q mutant of pyp
1t1c		Late intermediate il3 from time-resolved crystallography of the e46q mutant of pyp
1ts0		Structure of the pb1 intermediate from time-resolved laue crystallography
1ts6		Structure of the pb2 intermediate from time-resolved laue crystallography
1ts7		Structure of the pr cis wobble and pr e46q intermediates from time-resolved laue crystallography
1ts8		Structure of the pr cis planar intermediate from time- resolved laue crystallography
1ugu		Crystal structure of pyp e46q mutant
1uwn		The initial events in the photocycle of photoactive yellow protein: a common mechanism on light activation in photoreceptor proteins
1uwp		Initial events in the photocycle of photoactive yellow protein
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
1xfn		Nmr structure of the ground state of the photoactive yellow protein lacking the n-terminal part
1xfq		Structure of the blue shifted intermediate state of the photoactive yellow protein lacking the n-terminal part
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
1ztu		Structure of the chromophore binding domain of bacterial phytochrome
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
2d01		Wild type photoactive yellow protein, p65 form
2d02		R52q mutant of photoactive yellow protein, p65 form
2gj3		Crystal structure of the fad-containing pas domain of the protein nifl from azotobacter vinelandii.
2hv1		Haddock structure of arnt pas-b homodimer
2i9v		Structural role of y98 in pyp: effects on fluorescence, gateway and photocycle recovery
2jhe		N-terminal domain of tyrr transcription factor (residues 1 - 190)
2k7s		Human arnt c-terminal pas domain, 3 residue ib slip
2o9b		Crystal structure of bacteriophytochrome chromophore binding domain
2o9c		Crystal structure of bacteriophytochrome chromophore binding domain at 1.45 angstrom resolution
2ohh		Crystal structure of coenzyme f420h2 oxidase (fpra), a diiron flavoprotein, active oxidized state
2ohi		Crystal structure of coenzyme f420h2 oxidase (fpra), a diiron flavoprotein, reduced state
2ohj		Crystal structure of coenzyme f420h2 oxidase (fpra), a diiron flavoprotein, inactive oxidized state
2owh		Structure of an early-microsecond photolyzed state of co- bjfixlh
2owj		Structure of an early-microsecond photolyzed state of co- bjfixlh, dark state
2phy		Photoactive yellow protein, dark state (unbleached)
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)
2pyp		Photoactive yellow protein, photostationary state, 50% ground state, 50% bleached
2pyr		Photoactive yellow protein, 1 nanosecond intermediate (287k)
2qj5		Pyp ultra-high resolution of a bacterial photoreceptor
2qj7		Pyp ultra-high resolution of a bacterial photoreceptor
2qws		Neutron and x-ray structural studies of short hydrogen bonds in photoactive yellow protein (pyp)
2r78		Crystal structure of a domain of the sensory box sensor histidine kinase/response regulator from geobacter sulfurreducens
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))
2vea		The complete sensory module of the cyanobacterial phytochrome cph1 in the pr-state.
2vlg		Kina pas-a domain, homodimer
2vv6		Bjfixlh in ferric form
2vv7		Bjfixlh in unliganded ferrous form
2vv8		Co-bound structure of bjfixlh
2w0n		Plasticity of pas domain and potential role for signal transduction in the histidine-kinase dcus
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
2zoh		X-ray crystal structure of photoactive yellow protein, wild type, at 295k
2zoi		Neutron crystal structure of photoactive yellow protein, wild type, at 295k
3a0r		Crystal structure of histidine kinase thka (tm1359) in complex with response regulator protein trra (tm1360)
3a0s		Pas domain of histidine kinase thka (tm1359)
3a0v		Pas domain of histidine kinase thka (tm1359) (semet, f486m/f489m)
3b33		Crystal structure of the pas domain of nitrogen regulation protein nr(ii) from vibrio parahaemolyticus
3bwl		Crystal structure of pas domain of htr-like protein from haloarcula marismortui
3eeh		The crystal structure of the domain of the putative light and redox sensing histidine kinase from haloarcula marismortui
3ef0		The structure of fcp1, an essential rna polymerase ii ctd phosphatase
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
3fc7		The crystal structure of a domain of htr-like protein from haloarcula marismortui atcc 43049
3fg8		Crystal structure of pas domain of rha05790
3gdi		Mammalian clock protein mper2 - crystal struture of a pas domain fragment
3gec		Crystal structure of a tandem pas domain fragment of drosophila period
3phy		Photoactive yellow protein, dark state (unbleached), solution structure, nmr, 26 structures
3pyp		Photoactive yellow protein, cryotrapped early light cycle intermediate

Links (links to other resources describing this domain)
INTERPRO IPR000014