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167  structures 3562  species 7  interactions 21613  sequences 4071  architectures

Family: PAS (PF00989)

Summary: PAS fold

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This is the Wikipedia entry entitled "PAS domain". More...

PAS domain Edit Wikipedia article

PAS fold
FixL 1y28.png
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).
Symbol PAS
Pfam PF00989
InterPro IPR013767
SCOP 2phy
CDD cd00130

The PAS domain is a protein domain contained in many signaling proteins where it functions as a signal sensor.[2][3] PAS domains are found in a large number of organisms from bacteria to humans. The PAS domain was named after the three proteins in which it was first discovered:

Many PAS-domain proteins detect their signal by way of an associated cofactor such as heme.[4] Proteins that contain a PAS domain include Hypoxia-inducible factors.


  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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ Gilles-Gonzalez MA, Gonzalez G (February 2004). "Signal transduction by heme-containing PAS-domain proteins". J. Appl. Physiol. 96 (2): 774–83. doi:10.1152/japplphysiol.00941.2003. PMID 14715687. 

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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

  1. 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

  2. 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

  3. Ponting CP, Aravind L; , Curr Biol 1997;7:674-677.: PAS: a multifunctional domain family comes to light. PUBMED:9382818 EPMC:9382818

  4. 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

External database links

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.

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


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Curation and family details

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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 View help on HMM parameters

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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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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

PAS_11 PAS_11 Response_reg HisKA HLH PAS HATPase_c


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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