Biology:PAS domain

From HandWiki
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
SymbolPAS
PfamPF00989
Pfam clanCL0183
InterProIPR013767
SMARTPAS
PROSITEPDOC50112
SCOP22phy / SCOPe / SUPFAM
CDDcd00130

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]

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: Biology: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: Biology: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: Biology: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]

GAF domain

GAF domain
Identifiers
SymbolGAF
Pfam clanCL0161

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
SymbolCache
Pfam clanCL0165

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
SymbolHpt
PfamPF01627
InterProIPR036641

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
SymbolHAMP
PfamPF00672
Pfam clanCL0681
InterProIPR003660

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​; "A distal arginine in oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure". Biochemistry 42 (25): 7701–8. July 2003. doi:10.1021/bi0343370. PMID 12820879. https://escholarship.org/uc/item/0201b75s. 
  2. ↑ "Ligand-binding PAS domains in a genomic, cellular, and structural context". Annual Review of Microbiology 65: 261–286. 1 January 2011. doi:10.1146/annurev-micro-121809-151631. PMID 21663441. 
  3. ↑ "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. October 2015. doi:10.1107/S139900471501384X. PMID 26457436. Bibcode: 2015AcCrD..71.2127L. 
  4. ↑ "Structure and signaling mechanism of Per-ARNT-Sim domains". Structure 17 (10): 1282–1294. October 2009. doi:10.1016/j.str.2009.08.011. PMID 19836329. 
  5. ↑ 5.0 5.1 "Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2". PLOS Biology 7 (4). April 2009. doi:10.1371/journal.pbio.1000094. PMID 19402751. 
  6. ↑ "PAS: a multifunctional domain family comes to light". Current Biology 7 (11): R674–R677. November 1997. doi:10.1016/S0960-9822(06)00352-6. PMID 9382818. 
  7. ↑ "The PAS fold. A redefinition of the PAS domain based upon structural prediction". European Journal of Biochemistry 271 (6): 1198–1208. March 2004. doi:10.1111/j.1432-1033.2004.04023.x. PMID 15009198. 
  8. ↑ "Structure and signaling mechanism of Per-ARNT-Sim domains". Structure 17 (10): 1282–1294. October 2009. doi:10.1016/j.str.2009.08.011. PMID 19836329. 
  9. ↑ "Molecular genetics of the fruit-fly circadian clock". European Journal of Human Genetics 14 (6): 729–738. June 2006. doi:10.1038/sj.ejhg.5201547. PMID 16721409. 
  10. ↑ 10.0 10.1 10.2 10.3 "Ligand-binding PAS domains in a genomic, cellular, and structural context". Annual Review of Microbiology 65: 261–286. 1 January 2011. doi:10.1146/annurev-micro-121809-151631. PMID 21663441. 
  11. ↑ "Structure and signaling mechanism of Per-ARNT-Sim domains". Structure 17 (10): 1282–1294. October 2009. doi:10.1016/j.str.2009.08.011. PMID 19836329. 
  12. ↑ 12.0 12.1 "Mammalian Per-Arnt-Sim proteins in environmental adaptation". Annual Review of Physiology 72: 625–645. 2010. doi:10.1146/annurev-physiol-021909-135922. PMID 20148691. 
  13. ↑ "Molecular bases of circadian rhythms". Annual Review of Cell and Developmental Biology 17: 215–253. 28 November 2003. doi:10.1146/annurev.cellbio.17.1.215. PMID 11687489. 
  14. ↑ "ZEITLUPE encodes a novel clock-associated PAS protein from Arabidopsis". Cell 101 (3): 319–329. April 2000. doi:10.1016/S0092-8674(00)80841-7. PMID 10847686. 
  15. ↑ "A clock shock: mouse CLOCK is not required for circadian oscillator function". Neuron 50 (3): 465–477. May 2006. doi:10.1016/j.neuron.2006.03.041. PMID 16675400. 
  16. ↑ "An overview of the basic helix-loop-helix proteins". Genome Biology 5 (6): 226. 1 January 2004. doi:10.1186/gb-2004-5-6-226. PMID 15186484. 
  17. ↑ "Hypoxia-inducible factor-1 (HIF-1)". Molecular Pharmacology 70 (5): 1469–1480. November 2006. doi:10.1124/mol.106.027029. PMID 16887934. 
  18. ↑ "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. June 1995. doi:10.1073/pnas.92.12.5510. PMID 7539918. Bibcode: 1995PNAS...92.5510W. 
  19. ↑ "Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor". The EMBO Journal 19 (20): 5288–5299. October 2000. doi:10.1093/emboj/19.20.5288. PMID 11032796. 
  20. ↑ 20.0 20.1 "Novel domains of the prokaryotic two-component signal transduction systems". FEMS Microbiology Letters 203 (1): 11–21. September 2001. doi:10.1016/S0378-1097(01)00326-3. PMID 11557134. 
  21. ↑ "The GAF domain: an evolutionary link between diverse phototransducing proteins". Trends in Biochemical Sciences 22 (12): 458–459. December 1997. doi:10.1016/s0968-0004(97)01148-1. PMID 9433123. 
  22. ↑ 22.0 22.1 "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). April 2016. doi:10.1371/journal.pcbi.1004862. PMID 27049771. 
  23. ↑ "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. November 2000. doi:10.1016/S0968-0004(00)01672-8. PMID 11084361. 
  24. ↑ "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. July 1999. doi:10.1016/s0378-1097(99)00197-4. PMID 10418137. 
  25. ↑ "The HAMP domain structure implies helix rotation in transmembrane signaling". Cell 126 (5): 929–40. September 2006. doi:10.1016/j.cell.2006.06.058. PMID 16959572. 



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