|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 (; 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:
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)|
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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)
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% proteins involved KEGG pathway ID Description 62.41 map02020 Two-component system - General 21.07 map02030 Bacterial chemotaxis - General 4.56 map04710 Circadian rhythm 3.65 map05211 Renal cell carcinoma 2.53 map03090 Type II secretion system 1.72 map00230 Purine metabolism 1.32 map04914 Progesterone-mediated oocyte maturation 1.01 map04150 mTOR signaling pathway 0.20 map00562 Inositol phosphate metabolism 0.20 map04540 Gap junction 0.20 map00632 Benzoate degradation via CoA ligation 0.20 map00540 Lipopolysaccharide biosynthesis 0.20 map04730 Long-term depression 0.10 map00910 Nitrogen metabolism 0.10 map00190 Oxidative phosphorylation 0.10 map00130 Ubiquinone biosynthesis 0.10 map00400 Phenylalanine, tyrosine and tryptophan biosynthesis 0.10 map00790 Folate biosynthesis 0.10 map00340 Histidine metabolism 0.10 map00500 Starch and sucrose metabolism
This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with PAS domain which could be assigned to a KEGG orthologous group, and not all proteins containing PAS domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.
- 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)