PAS domain

PAS fold
Crystallographic structure of the PAS domain of the bacterial oxygen sensor protein fixL. [1] The protein is depicted as a rainbow colored cartoon (N-terminus = blue, C-terminus = red) while the heme ligand is shown as sticks (carbon = white, nitrogen = blue, oxygen = red, iron = orange).
Identifiers
Symbol	PAS
Pfam	PF00989
Pfam clan	CL0183
ECOD	223.1.1
InterPro	IPR013767
SMART	PAS
PROSITE	PDOC50112
SCOP2	2phy / SCOPe / SUPFAM
CDD	cd00130
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary PDB 1byw ​, 1d06 ​, 1d7e ​, 1dp6 ​, 1dp8 ​, 1dp9 ​, 1drm ​, 1ew0 ​, 1f98 ​, 1f9i ​, 1gsv ​, 1gsw ​, 1gsx ​, 1kou ​, 1ll8 ​, 1lsv ​, 1lsw ​, 1lsx ​, 1lt0 ​, 1mzu ​, 1nwz ​, 1odv ​, 1ot6 ​, 1ot9 ​, 1ota ​, 1otb ​, 1otd ​, 1ote ​, 1oti ​, 1s1y ​, 1s1z ​, 1s4r ​, 1s4s ​, 1s66 ​, 1s67 ​, 1t18 ​, 1t19 ​, 1t1a ​, 1t1b ​, 1t1c ​, 1ts0 ​, 1ts6 ​, 1ts7 ​, 1ts8 ​, 1ugu ​, 1uwn ​, 1uwp ​, 1v9y ​, 1v9z ​, 1vb6 ​, 1wa9 ​, 1xfn ​, 1xfq ​, 1xj2 ​, 1xj3 ​, 1xj4 ​, 1xj6 ​, 1y28 ​, 2d01 ​, 2d02 ​, 2phy ​, 2pyp ​, 2pyr ​, 3phy ​, 3pyp ​

A Per-Arnt-Sim (PAS) domain is a protein domain found in all kingdoms of life. ^[2] Generally, the PAS domain acts as a molecular sensor, whereby small molecules and other proteins associate via binding of the PAS domain. ^{[3] [4] [5]} Due to this sensing capability, the PAS domain has been shown as the key structural motif involved in protein-protein interactions of the circadian clock, and it is also a common motif found in signaling proteins, where it functions as a signaling sensor. ^{[6] [7]}

Discovery

PAS domains are found in a large number of organisms from bacteria to mammals. The PAS domain was named after the three proteins in which it was first discovered: ^[8]

• Per – period circadian protein
• Arnt – aryl hydrocarbon receptor nuclear translocator protein
• Sim – single-minded protein

Since the initial discovery of the PAS domain, a large quantity of PAS domain binding sites have been discovered in bacteria and eukaryotes. A subset called PAS LOV proteins are responsive to oxygen, light and voltage. ^[9]

Structure

Although the PAS domain exhibits a degree of sequence variability, the three-dimensional structure of the PAS domain core is broadly conserved. ^[10] This core consists of a five-stranded antiparallel β-sheet and several α-helices. Structural changes, as a result of signaling, predominantly originate within the β-sheet. These signals propagate via the α-helices of the core to the covalently-attached effector domain. ^[11] In 1998, the PAS domain core architecture was first characterized in the structure of photoactive yellow protein (PYP) from Halorhodospira halophila . ^[10] In many proteins, a dimer of PAS domains is required, whereby one binds a ligand and the other mediates interactions with other proteins. ^[5]

Examples of PAS in organisms

The PAS domains that are known share less than 20% average pairwise sequence identity, meaning they are surprisingly dissimilar. ^[10] PAS domains are frequently found on proteins with other environmental sensing mechanisms. Also, many PAS domains are attached to photoreceptive cells. ^[12]

Bacteria

Often in the bacterial kingdom, PAS domains are positioned at the amino terminus of signaling proteins such as sensor histidine kinases, cyclic-di-GMP syntheses and hydrolases, and methyl-accepting chemotaxis proteins. ^[10]

Neurospora

Main article: Neurospora

In the presence of light, White Collar-1 (WC-1) and White Collar-2 (WC-2) dimerizes via mediation by the PAS domains, which activates translation of FRQ. ^[13]

Drosophila

Main article: Drosophila

In the presence of light, CLK and CYC attach via a PAS domain, activating the translation of PER, which then associates to Tim via the PER PAS domain. The following genes contain PAS binding domains: PER, Tim, CLK, CYC.

Arabidopsis

Main article: Arabidopsis

A PAS domain is found in the ZTL and NPH1 genes. These domains are very similar to the PAS domain found in the Neurospora circadian-associated protein WC-1. ^[14]

Mammals

The circadian clock that is currently understood for mammals begins when light activates BMAL1 and CLK to bind via their PAS domains. That activator complex regulates Per1, Per2, and Per3 which all have PAS domains that are used to bind to cryptochromes 1 and 2 (CRY 1,2 family). The following mammalian genes contain PAS binding domains: Per1, Per2, Per3, Cry1, Cry2, Bmal, Clk, Pasd1.

Other mammalian PAS roles

Within Mammals, both PAS domains play important roles. PAS A is responsible for the protein-protein interactions with other PAS domain proteins, while PAS B has a more versatile role. It mediates interactions with chaperonins and other small molecules like dioxin, but PAS B domains in NPAS2, a homolog of the Drosophila clk gene, and the hypoxia inducible factor (HIF) also help to mediate ligand binding. ^[12] Furthermore, PAS domains containing the NPAS2 protein have been shown to be a substitute for the Clock gene in mutant mice who lack the Clock gene completely. ^[15]

The PAS domain also directly interacts with BHLH. It is typically located on the C-Terminus of the BHLH protein. PAS domains containing BHLH proteins form a BHLH-Pas protein, typically found and encoded in HIF, which require both the PAS domain and BHLH domain and the Clock gene. ^{[16] [17] [18]}

Related sensor domains

GAF domain

GAF domain
Identifiers
Symbol	GAF
Pfam clan	CL0161
ECOD	223.1.1

These cGMP-binding domains are found in diverse phototransducing proteins across eukaryotes and eubacteria. They are present in plant and cyanobacterial phytochromes, vertebrate and invertebrate cGMP-stimulated phosphodiesterases (PDEs) and some non-photosynthetic eubacteria. ^{[19] [20] [21]}

Cache domain

Cache domain
Identifiers
Symbol	Cache
Pfam clan	CL0165
ECOD	223.1.1

These extracellular signaling domains are homologous to PAS domains but distinct. ^[22] They are common to animal calcium (Ca2+) channel subunits and certain prokaryotic chemotaxis receptors and play a role in small-molecule recognition across various species, suggesting a conserved mechanism of ligand binding. ^[23] As opposite to the intracellular PAS and GAF domains, they show a long extra N-terminal alpha helix. ^[22]

Other sensor domains

Hpt domain

Hpt domain
Identifiers
Symbol	Hpt
Pfam	PF01627
ECOD	601.3.1
InterPro	IPR036641
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Also known as histidine phosphotransfer domains and histidine phosphotransferases, these domains are protein domains involved in the "phosphorelay" form of two-component regulatory systems. ^[20]

HAMP domain

HAMP
Identifiers
Symbol	HAMP
Pfam	PF00672
Pfam clan	CL0681
ECOD	4168.1.1
InterPro	IPR003660
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

The HAMP domain (present in Histidine kinases, Adenylate cyclases, Methyl accepting proteins and Phosphatases) ^[24] is an approximately 50-amino acid alpha-helical region that forms a dimeric, four-helical coiled coil. ^[25]

References

1. PDB: 1y28 ​; Dunham CM, Dioum EM, Tuckerman JR, Gonzalez G, Scott WG, Gilles-Gonzalez MA (July 2003). "A distal arginine in oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure". Biochemistry. 42 (25): 7701–8. doi:10.1021/bi0343370. PMID   12820879. S2CID   14090693.
2. Henry JT, Crosson S (1 January 2011). "Ligand-binding PAS domains in a genomic, cellular, and structural context". Annual Review of Microbiology. 65: 261–286. doi:10.1146/annurev-micro-121809-151631. PMC   3298442 . PMID   21663441.
3. Liu YC, Machuca MA, Beckham SA, Gunzburg MJ, Roujeinikova A (October 2015). "Structural basis for amino-acid recognition and transmembrane signalling by tandem Per-Arnt-Sim (tandem PAS) chemoreceptor sensory domains". Acta Crystallographica. Section D, Biological Crystallography. 71 (Pt 10): 2127–2136. Bibcode:2015AcCrD..71.2127L. doi:10.1107/S139900471501384X. PMID   26457436.
4. Möglich A, Ayers RA, Moffat K (October 2009). "Structure and signaling mechanism of Per-ARNT-Sim domains". Structure. 17 (10): 1282–1294. doi:10.1016/j.str.2009.08.011. PMC   3092527 . PMID   19836329.
5. Hennig S, Strauss HM, Vanselow K, Yildiz O, Schulze S, Arens J, et al. (April 2009). "Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2". PLOS Biology. 7 (4) e94. doi: 10.1371/journal.pbio.1000094 . PMC   2671562 . PMID   19402751.
6. Ponting CP, Aravind L (November 1997). "PAS: a multifunctional domain family comes to light". Current Biology. 7 (11): R674 –R677. doi: 10.1016/S0960-9822(06)00352-6 . PMID   9382818. S2CID   14105830.
7. Hefti MH, Françoijs KJ, de Vries SC, Dixon R, Vervoort J (March 2004). "The PAS fold. A redefinition of the PAS domain based upon structural prediction". European Journal of Biochemistry. 271 (6): 1198–1208. doi: 10.1111/j.1432-1033.2004.04023.x . PMID   15009198.
8. Möglich A, Ayers RA, Moffat K (October 2009). "Structure and signaling mechanism of Per-ARNT-Sim domains". Structure. 17 (10): 1282–1294. doi:10.1016/j.str.2009.08.011. PMC   3092527 . PMID   19836329.
9. Rosato E, Tauber E, Kyriacou CP (June 2006). "Molecular genetics of the fruit-fly circadian clock". European Journal of Human Genetics. 14 (6): 729–738. doi: 10.1038/sj.ejhg.5201547 . PMID   16721409.
10. Henry JT, Crosson S (1 January 2011). "Ligand-binding PAS domains in a genomic, cellular, and structural context". Annual Review of Microbiology. 65: 261–286. doi:10.1146/annurev-micro-121809-151631. PMC   3298442 . PMID   21663441.
11. Möglich A, Ayers RA, Moffat K (October 2009). "Structure and signaling mechanism of Per-ARNT-Sim domains". Structure. 17 (10): 1282–1294. doi:10.1016/j.str.2009.08.011. PMC   3092527 . PMID   19836329.
12. McIntosh BE, Hogenesch JB, Bradfield CA (2010). "Mammalian Per-Arnt-Sim proteins in environmental adaptation". Annual Review of Physiology. 72: 625–645. doi:10.1146/annurev-physiol-021909-135922. PMID   20148691.
13. Harmer SL, Panda S, Kay SA (28 November 2003). "Molecular bases of circadian rhythms". Annual Review of Cell and Developmental Biology. 17: 215–253. doi:10.1146/annurev.cellbio.17.1.215. PMID   11687489.
14. Somers DE, Schultz TF, Milnamow M, Kay SA (April 2000). "ZEITLUPE encodes a novel clock-associated PAS protein from Arabidopsis". Cell. 101 (3): 319–329. doi: 10.1016/S0092-8674(00)80841-7 . PMID   10847686. S2CID   3013788.
15. Debruyne JP, Noton E, Lambert CM, Maywood ES, Weaver DR, Reppert SM (May 2006). "A clock shock: mouse CLOCK is not required for circadian oscillator function". Neuron. 50 (3): 465–477. doi: 10.1016/j.neuron.2006.03.041 . PMID   16675400. S2CID   19028601.
16. Jones S (1 January 2004). "An overview of the basic helix-loop-helix proteins". Genome Biology. 5 (6): 226. doi: 10.1186/gb-2004-5-6-226 . PMC   463060 . PMID   15186484.
17. Ke Q, Costa M (November 2006). "Hypoxia-inducible factor-1 (HIF-1)". Molecular Pharmacology. 70 (5): 1469–1480. doi:10.1124/mol.106.027029. PMID   16887934. S2CID   2522614.
18. Wang GL, Jiang BH, Rue EA, Semenza GL (June 1995). "Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension". Proceedings of the National Academy of Sciences of the United States of America. 92 (12): 5510–5514. Bibcode:1995PNAS...92.5510W. doi: 10.1073/pnas.92.12.5510 . PMC   41725 . PMID   7539918.
19. Ho YS, Burden LM, Hurley JH (October 2000). "Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor". The EMBO Journal. 19 (20): 5288–5299. doi:10.1093/emboj/19.20.5288. PMC   314001 . PMID   11032796.
20. Galperin MY, Nikolskaya AN, Koonin EV (September 2001). "Novel domains of the prokaryotic two-component signal transduction systems". FEMS Microbiology Letters. 203 (1): 11–21. doi:10.1016/S0378-1097(01)00326-3. PMID   11557134.
21. Aravind L, Ponting CP (December 1997). "The GAF domain: an evolutionary link between diverse phototransducing proteins". Trends in Biochemical Sciences. 22 (12): 458–459. doi:10.1016/s0968-0004(97)01148-1. PMID   9433123.
22. Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB (April 2016). "Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes". PLOS Computational Biology. 12 (4) e1004862. doi: 10.1371/journal.pcbi.1004862 . PMC   4822843 . PMID   27049771.
23. Anantharaman V, Aravind L (November 2000). "Cache - a signaling domain common to animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors". Trends in Biochemical Sciences. 25 (11): 535–537. doi:10.1016/S0968-0004(00)01672-8. PMID   11084361.
24. Aravind L, Ponting CP (July 1999). "The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins". FEMS Microbiology Letters. 176 (1): 111–6. doi: 10.1016/s0378-1097(99)00197-4 . PMID   10418137.
25. Hulko M, Berndt F, Gruber M, Linder JU, Truffault V, Schultz A, et al. (September 2006). "The HAMP domain structure implies helix rotation in transmembrane signaling". Cell. 126 (5): 929–40. doi: 10.1016/j.cell.2006.06.058 . PMID   16959572. S2CID   18396561.