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208  structures 6771  species 0  interactions 58225  sequences 7432  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
Identifiers
SymbolPAS
PfamPF00989
InterProIPR013767
SCOP22phy / SCOPe / SUPFAM

The PAS domain is a protein domain contained in many signalling proteins where they are used as a signal sensor.[1][2] PAS domains are found in a large number of organisms from bacteria to humans. The PAS domain was named after three proteins that it occurs in:

Many PAS-domain proteins detect their signal by way of an associated cofactor such as heme.[3]

References

  1. ^ Ponting CP, Aravind L (1997). "PAS: a multifunctional domain family comes to light". Curr. Biol. 7 (11): R674–7. PMID 9382818. {{cite journal}}: Unknown parameter |month= ignored (help)
  2. ^ Hefti MH, Françoijs KJ, de Vries SC, Dixon R, Vervoort J (2004). "The PAS fold. A redefinition of the PAS domain based upon structural prediction". Eur. J. Biochem. 271 (6): 1198–208. PMID 15009198. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ Gilles-Gonzalez MA, Gonzalez G (2004). "Signal transduction by heme-containing PAS-domain proteins". J. Appl. Physiol. 96 (2): 774–83. doi:10.1152/japplphysiol.00941.2003. PMID 14715687. {{cite journal}}: Unknown parameter |month= ignored (help)

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

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).

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. Heme, 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 17 members:

AbfS_sensor CpxA_peri DUF5593 MEKHLA MLTR_LBD PAS PAS_10 PAS_11 PAS_12 PAS_2 PAS_3 PAS_4 PAS_5 PAS_6 PAS_7 PAS_8 PAS_9

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(49)
Full
(58225)
Representative proteomes UniProt
(227090)
RP15
(7367)
RP35
(25421)
RP55
(53716)
RP75
(87883)
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PP/heatmap 1            

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

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(49)
Full
(58225)
Representative proteomes UniProt
(227090)
RP15
(7367)
RP35
(25421)
RP55
(53716)
RP75
(87883)
Alignment:
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Order:
Sequence:
Gaps:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(49)
Full
(58225)
Representative proteomes UniProt
(227090)
RP15
(7367)
RP35
(25421)
RP55
(53716)
RP75
(87883)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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.

Note: You can also download the data file for the tree.

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 View help on the curation process

Seed source: Sequences from SMART alignment
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 49
Number in full: 58225
Average length of the domain: 104 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 15.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -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: 28
Download: download the raw HMM for this family

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

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 208 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044QM06 View 3D Structure Click here
A0A044QT91 View 3D Structure Click here
A0A077YZS5 View 3D Structure Click here
A0A077Z924 View 3D Structure Click here
A0A077Z9V9 View 3D Structure Click here
A0A077ZEG6 View 3D Structure Click here
A0A077ZF75 View 3D Structure Click here
A0A077ZII7 View 3D Structure Click here
A0A0D2H214 View 3D Structure Click here
A0A0H3GNY2 View 3D Structure Click here
A0A0H3GPD8 View 3D Structure Click here
A0A0H3GPJ3 View 3D Structure Click here
A0A0H3GXU8 View 3D Structure Click here
A0A0H3GZ10 View 3D Structure Click here
A0A0K0E7J2 View 3D Structure Click here
A0A0K0E825 View 3D Structure Click here
A0A0K0E9T6 View 3D Structure Click here
A0A0K0ELF8 View 3D Structure Click here
A0A0K0ERF6 View 3D Structure Click here
A0A0N4UF75 View 3D Structure Click here
A0A0N4UFL6 View 3D Structure Click here
A0A0N4UM22 View 3D Structure Click here
A0A0P0Y5C3 View 3D Structure Click here
A0A0R0GET9 View 3D Structure Click here
A0A0R0HSY5 View 3D Structure Click here
A0A0R0KN47 View 3D Structure Click here
A0A0R4IBR4 View 3D Structure Click here
A0A0R4IH97 View 3D Structure Click here
A0A0R4IY58 View 3D Structure Click here
A0A158N8K8 View 3D Structure Click here
A0A158Q530 View 3D Structure Click here
A0A175VVQ3 View 3D Structure Click here
A0A1C1CN95 View 3D Structure Click here
A0A1D6G6Q3 View 3D Structure Click here
A0A1D6GGX9 View 3D Structure Click here
A0A1D6HRS3 View 3D Structure Click here
A0A1D6INR5 View 3D Structure Click here
A0A1D6KD94 View 3D Structure Click here
A0A1D6MX83 View 3D Structure Click here
A0A1D6Q065 View 3D Structure Click here