Summary: PAS fold

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PAS domain Edit Wikipedia article

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

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

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 velcro, whereby small molecules and other proteins associate via binding of the PAS domain.^[3]^[4]^[5] Due to this velcro 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 Halorhodospira halophila photoactive yellow protein (PYP).^[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 synthases and hydrolases, and methyl-accepting chemotaxis proteins.^[10]

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

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

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.

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]

References

^ 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.
^ Henry, Jonathan T.; Crosson, Sean (1 January 2011). "Ligand-binding PAS domains in a genomic, cellular, and structural context". Annual Review of Microbiology. pp. 261–286. doi:10.1146/annurev-micro-121809-151631.
^ Liu, Yu C.; Machuca, Mayra A.; Beckham, Simone A.; Gunzburg, Menachem J.; Roujeinikova, Anna (1 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. pp. 2127–2136. doi:10.1107/S139900471501384X.
^ Möglich, Andreas; Ayers, Rebecca A.; Moffat, Keith (14 October 2009). "Structure and signaling mechanism of Per-ARNT-Sim domains". Structure (London, England: 1993). pp. 1282–1294. doi:10.1016/j.str.2009.08.011.
^ ^a ^b Hennig, Sven; Strauss, Holger M.; Vanselow, Katja; Yildiz, Özkan; Schulze, Sabrina; Arens, Julia; Kramer, Achim; Wolf, Eva (28 April 2009). "Structural and Functional Analyses of PAS Domain Interactions of the Clock Proteins Drosophila PERIOD and Mouse PERIOD2". PLOS Biology. pp. e1000094. doi:10.1371/journal.pbio.1000094.
^ Ponting CP, Aravind L (November 1997). "PAS: a multi-functional domain family comes to light". Curr. Biol. 7 (11): R674–7. doi:10.1016/S0960-9822(06)00352-6. PMID 9382818.
^ 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". Eur. J. Biochem. 271 (6): 1198–208. doi:10.1111/j.1432-1033.2004.04023.x. PMID 15009198.
^ Möglich, Andreas; Ayers, Rebecca A.; Moffat, Keith (14 October 2009). "Structure and Signaling Mechanism of Per-ARNT-Sim Domains". Structure (London, England : 1993). pp. 1282–1294. doi:10.1016/j.str.2009.08.011.
^ Rosato, Ezio; Tauber, Eran; Kyriacou, Charalambos P. (1 January 2006). "Molecular genetics of the fruit-fly circadian clock". European Journal of Human Genetics. pp. 729–738. doi:10.1038/sj.ejhg.5201547.
^ ^a ^b ^c ^d Henry, Jonathan T.; Crosson, Sean (1 January 2011). "Ligand-Binding PAS Domains in a Genomic, Cellular, and Structural Context". Annual Review of Microbiology. pp. 261–286. doi:10.1146/annurev-micro-121809-151631.
^ "Structure and Signaling Mechanism of Per-ARNT-Sim Domains" (PDF).
^ ^a ^b McIntosh, Brian; Hogenesch, John; Bradfield, Christopher. "Mammalian Per-Arnt-Sim Proteins in Environmental Adaptation | Annual Review of Physiology". Annual Review of Physiology. doi:10.1146/annurev-physiol-021909-135922#_i21.
^ Harmer, Stacey L.; Panda, Satchidananda; Kay, Steve A. (28 November 2003). "Molecular Bases of Circadian Rhythms". Annual Review of Cell and Developmental Biology. pp. 215–253. doi:10.1146/annurev.cellbio.17.1.215.
^ Somers, David; Schultz, Thomas; Kay, Steve; Milnamow, Maureen. "ZEITLUPE Encodes a Novel Clock-Associated PAS Protein from Arabidopsis". ScienceDirect. Cell. doi:10.1016/S0092-8674(00)80841-7.
^ 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): 465–77. doi:10.1016/j.neuron.2006.03.041. PMID 16675400.
^ Jones, Susan (1 January 2004). "An overview of the basic helix-loop-helix proteins". Genome Biology. p. 226. doi:10.1186/gb-2004-5-6-226.
^ Ke, Qingdong; Costa, Max (1 November 2006). "Hypoxia-Inducible Factor-1 (HIF-1)". Molecular Pharmacology. pp. 1469–1480. doi:10.1124/mol.106.027029.
^ Wang, G. L.; Jiang, B. H.; Rue, E. A.; Semenza, G. L. (6 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. pp. 5510–5514.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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PAS fold Provide feedback

The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya.

Literature references

Zhulin IB, Taylor BL, Dixon R; , Trends Biochem Sci 1997;22:331-333.: PAS domain S-boxes in archaea, bacteria and sensors for oxygen and redox. PUBMED:9301332 EPMC:9301332
Borgstahl GE, Williams DR, Getzoff ED; , Biochemistry 1995;34:6278-6287.: 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. PUBMED:7756254 EPMC:7756254
Ponting CP, Aravind L; , Curr Biol 1997;7:674-677.: PAS: a multifunctional domain family comes to light. PUBMED:9382818 EPMC:9382818
Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J; , Eur J Biochem 2004;271:1198-1208.: The PAS fold: a redefination of the PAS domain based upon structural prediction. PUBMED:15009198 EPMC:15009198

Internal database links

SCOOP:	dCache_1 IncA MEKHLA PAS_10 PAS_11 PAS_2 PAS_3 PAS_4 PAS_7 PAS_8 PAS_9 sCache_3_3 SpoVT_C STAS
Similarity to PfamA using HHSearch:	PAS_2 PAS_3 PAS_4 PAS_7 PAS_8 PAS_9 PAS_10 PAS_11

External database links

HOMSTRAD:	PAS
SCOP:	2phy
SMART:	PAS

This tab holds annotation information from the InterPro database.

InterPro entry IPR013767

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 INTERPRO. 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].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Biological process

regulation of transcription, DNA-templated (GO:0006355)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PAS_Fold (CL0183), which has the following description:

This clan contains PAS domains that are found in a wide variety of bacterial signaling proteins.

The clan contains the following 13 members:

CpxA_peri MEKHLA PAS PAS_10 PAS_11 PAS_2 PAS_3 PAS_4 PAS_5 PAS_6 PAS_7 PAS_8 PAS_9

Alignments

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	Seed (49)	Full (21613)	Representative proteomes				UniProt (59725)	NCBI (320287)	Meta (3365)
	Seed (49)	Full (21613)	RP15 (4367)	RP35 (12153)	RP55 (20833)	RP75 (31126)	UniProt (59725)	NCBI (320287)	Meta (3365)
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HTML	View
PP/heatmap	₁

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (49)	Full (21613)	Representative proteomes				UniProt (59725)	NCBI (320287)	Meta (3365)
	Seed (49)	Full (21613)	RP15 (4367)	RP35 (12153)	RP55 (20833)	RP75 (31126)	UniProt (59725)	NCBI (320287)	Meta (3365)
Alignment:
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Sequence:	Inserts lower case All upper case
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	Seed (49)	Full (21613)	Representative proteomes				UniProt (59725)	NCBI (320287)	Meta (3365)
	Seed (49)	Full (21613)	RP15 (4367)	RP35 (12153)	RP55 (20833)	RP75 (31126)	UniProt (59725)	NCBI (320287)	Meta (3365)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download		Download
Gzipped	Download	Download	Download	Download	Download	Download	Download		Download

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Sequences from SMART alignment

Previous IDs:

none

Type:

Domain

Author:

Bateman A

Number in seed:

49

Number in full:

21613

Average length of the domain:

104.70 aa

Average identity of full alignment:

15 %

Average coverage of the sequence by the domain:

15.95 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	22.6	22.6
Trusted cut-off	22.6	22.6
Noise cut-off	22.5	22.5

Model length:

113

Family (HMM) version:

24

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Species distribution

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

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We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

There are 7 interactions for this family. More...

PAS Response_reg HATPase_c HisKA PAS_11 PAS_11 HLH

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PAS domain has been found. There are 167 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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v t e Protein domains

BAR BIR BZIP CARD C1 C2 DED ENTH FYVE HEAT Kringle LIM LRR NACHT PAS PDZ Pyrin PH PX SH2 SH3 SUN TRIO WD40 zinc finger

Family: PAS (PF00989)

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