Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
5  structures 976  species 0  interactions 1069  sequences 11  architectures

Family: SpoVT_C (PF15714)

Summary: Stage V sporulation protein T C-terminal, transcription factor

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

GAF domain Edit Wikipedia article

GAF domain
PDB 1mc0 EBI.jpg
3',5'-Cyclic Nucleotide Phosphodiesterase 2A, Containing the GAF A and GAF B Domains.[1]
Identifiers
Symbol GAF
Pfam PF01590
Pfam clan CL0161
InterPro IPR003018
SMART GAF
SCOP 1fl4
SUPERFAMILY 1fl4

The GAF domain is a type of protein domain that is found in a wide range of proteins from all species.[2] The GAF domain is named after some of the proteins it is found in: cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. The first structure of a GAF domain solved by Ho and colleagues showed that this domain shared a similar fold with the PAS domain.[3] In mammals, GAF domains are found in five members of the cyclic nucleotide phosphodiesterase superfamily: PDE2, PDE5, and PDE6 which bind cGMP to the GAF domain, PDE10 which binds cAMP, and PDE11 which binds both cGMP and cAMP.[4][5]

Examples

Human proteins containing this domain include:

References

  1. ^ Martinez SE, Wu AY, Glavas NA, Tang XB, Turley S, Hol WG, Beavo JA (October 2002). "The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding". Proceedings of the National Academy of Sciences of the United States of America. 99 (20): 13260–5. Bibcode:2002PNAS...9913260M. doi:10.1073/pnas.192374899. JSTOR 3073384. PMC 130621Freely accessible. PMID 12271124. 
  2. ^ Aravind L, Ponting CP (December 1997). "The GAF domain: an evolutionary link between diverse phototransducing proteins". Trends in Biochemical Sciences. 22 (12): 458–9. doi:10.1016/S0968-0004(97)01148-1. PMID 9433123. 
  3. ^ 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): 5288–99. doi:10.1093/emboj/19.20.5288. PMC 314001Freely accessible. PMID 11032796. 
  4. ^ Fawcett L, Baxendale R, Stacey P, McGrouther C, Harrow I, Soderling S, Hetman J, Beavo JA, Phillips SC (March 2000). "Molecular cloning and characterization of a distinct human phosphodiesterase gene family: PDE11A". Proceedings of the National Academy of Sciences of the United States of America. 97 (7): 3702–7. Bibcode:2000PNAS...97.3702F. doi:10.1073/pnas.050585197. JSTOR 121956. PMC 16303Freely accessible. PMID 10725373. 
  5. ^ Schultz JE (2009). "Structural and biochemical aspects of tandem GAF domains". Handbook of Experimental Pharmacology. Handbook of Experimental Pharmacology. 191 (191): 93–109. doi:10.1007/978-3-540-68964-5_6. ISBN 978-3-540-68960-7. PMID 19089327. 

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.

Stage V sporulation protein T C-terminal, transcription factor Provide feedback

SpoVT_C is the C-terminal part of the stage V sporulation protein T, a transcription factor involved in endospore formation in Gram-positive bacteria such as Bacillus subtilis. Sporulation is induced by conditions of environmental stress to protect the genome. SpoVT behaves as a tetramer that shows an overall significant distortion mediated by electrostatic interactions. Two monomers dimerise via the highly charged N-terminal AbrB-like domains, family PF04014 to form swapped-hairpin beta-barrels. These asymmetric dimers then form tetramers through the formation of mixed helix bundles between their C-terminal domains. The C-termini themselves fold as GAF (cGMP-specific and cGMP-stimulated phosphodiesterases, Anabaena adenylate cyclases, and Escherichia coli FhlA) domains [1].

Literature references

  1. Asen I, Djuranovic S, Lupas AN, Zeth K;, J Mol Biol. 2009;386:962-975.: Crystal structure of SpoVT, the final modulator of gene expression during spore development in Bacillus subtilis. PUBMED:18996130 EPMC:18996130


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR039472

This entry represents the C-terminal part of the stage V sporulation protein T, a transcription factor involved in endospore formation in Gram-positive bacteria such as Bacillus subtilis. Sporulation is induced by conditions of environmental stress to protect the genome. SpoVT behaves as a tetramer that shows an overall significant distortion mediated by electrostatic interactions. Two monomers dimerise via the highly charged N-terminal AbrB-like domains, INTERPRO, to form swapped-hairpin beta-barrels. These asymmetric dimers then form tetramers through the formation of mixed helix bundles between their C-terminal domains. The C-termini themselves fold as GAF (cGMP-specific and cGMP-stimulated phosphodiesterases, Anabaena adenylate cyclases, and Escherichia coli FhlA) domains [PUBMED:18996130].

This GAF domain can also be found in sensor protein LytS from Bacillus subtilis. LytS is a member of the two-component regulatory system LytS/LytT that probably regulates genes involved in cell wall metabolism [PUBMED:11717295].

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan GAF (CL0161), which has the following description:

A clan of related transcriptional regulator domains.

The clan contains the following 14 members:

Autoind_bind bHLH-MYC_N CCB2_CCB4 CodY DUF3369 DUF484 GAF GAF_2 GAF_3 Haem_degrading HrcA IclR PHY SpoVT_C

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(195)
Full
(1069)
Representative proteomes UniProt
(3841)
NCBI
(3863)
Meta
(16)
RP15
(181)
RP35
(683)
RP55
(1102)
RP75
(1645)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(195)
Full
(1069)
Representative proteomes UniProt
(3841)
NCBI
(3863)
Meta
(16)
RP15
(181)
RP35
(683)
RP55
(1102)
RP75
(1645)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(195)
Full
(1069)
Representative proteomes UniProt
(3841)
NCBI
(3863)
Meta
(16)
RP15
(181)
RP35
(683)
RP55
(1102)
RP75
(1645)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: COG2002
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 195
Number in full: 1069
Average length of the domain: 126.20 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 58.91 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.5 27.5
Trusted cut-off 27.5 27.5
Noise cut-off 27.4 27.4
Model length: 128
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 SpoVT_C domain has been found. There are 5 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.

Loading structure mapping...