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.
4  structures 141  species 0  interactions 164  sequences 1  architecture

Family: Sda (PF08970)

Summary: Sporulation inhibitor A

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 "Sda protein domain". More...

Sda protein domain Edit Wikipedia article

Sda
PDB 1pv0 EBI.jpg
structure of the sda antikinase
Identifiers
Symbol Sda
Pfam PF08970
InterPro IPR015064

In molecular biology, the protein domain Sda is short for suppressor of dnaA or otherwise known as sporulation inhibitor A. It is found only in bacteria. This protein domain is highly important to cell survival. When starved of nutrients, the cell is under extreme stress so undergoes a series of reactions to increase the chances of survival. One method is to form endospores which can withstand a large amount of environmental pressure.[1] Sda protein domain is a checkpoint which prevents the formation of spores. The Sda domain affects cell signalling. It prevents the cell communicating the stress that it is under, which is crucial if the cell is to survive.

Cell signalling

All cells communicate through cell signalling. The Sda protein domain inhibits the Histidine kinase signal transduction. This signal transduction mechanism is switched on when the cell is under stress, such as nutrient deprivation. It works through the kinase first autophosphorylating the Histidine residue and this triggers sporulation. Sda prevents this pathway from occurring by inhibiting the histidine kinase. More specifically, Sda can be considered an antikinase and binds to KinA. The Sda-KinA complex now physically blocks any phosphorylation of the Histidine Kinase residue.[2]

Function

These sporulation inhibitors are anti-kinases that bind to the histidine kinase KinA phosphotransfer protein domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation through the prevention of phosphorylation of spo0A, a transcription factor.[2]

Structure

Members of this protein group contain two antiparallel alpha helices that are linked by an inter-helix loop to form a helical hairpin. These monomers associate to form a simple trimeric arrangement.[3]

References

  1. ^ Burkholder WF, Kurtser I, Grossman AD (2001). "Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis.". Cell 104 (2): 269–79. doi:10.1016/s0092-8674(01)00211-2. PMID 11207367. 
  2. ^ a b Rowland SL, Burkholder WF, Cunningham KA, Maciejewski MW, Grossman AD, King GF (2004). "Structure and mechanism of action of Sda, an inhibitor of the histidine kinases that regulate initiation of sporulation in Bacillus subtilis.". Mol Cell 13 (5): 689–701. doi:10.1016/S1097-2765(04)00084-X. PMID 15023339. 
  3. ^ Jacques DA, Streamer M, Rowland SL, King GF, Guss JM, Trewhella J et al. (2009). "Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state.". Acta Crystallogr D Biol Crystallogr 65 (Pt 6): 574–81. doi:10.1107/S090744490901169X. PMC 2725781. PMID 19465772. 

This article incorporates text from the public domain Pfam and InterPro IPR015064


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.

Sporulation inhibitor A Provide feedback

Members of this protein family contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) [1].

Literature references

  1. Rowland SL, Burkholder WF, Cunningham KA, Maciejewski MW, Grossman AD, King GF; , Mol Cell. 2004;13:689-701.: Structure and mechanism of action of Sda, an inhibitor of the histidine kinases that regulate initiation of sporulation in Bacillus subtilis. PUBMED:15023339 EPMC:15023339


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015064

Members of this protein group contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) [PUBMED:15023339].

Domain organisation

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

Loading domain graphics...

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(18)
Full
(164)
Representative proteomes NCBI
(93)
Meta
(1)
RP15
(11)
RP35
(26)
RP55
(28)
RP75
(36)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(18)
Full
(164)
Representative proteomes NCBI
(93)
Meta
(1)
RP15
(11)
RP35
(26)
RP55
(28)
RP75
(36)
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
(18)
Full
(164)
Representative proteomes NCBI
(93)
Meta
(1)
RP15
(11)
RP35
(26)
RP55
(28)
RP75
(36)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: pdb_1pv0
Previous IDs: none
Type: Domain
Author: Mistry J, Sammut SJ
Number in seed: 18
Number in full: 164
Average length of the domain: 45.20 aa
Average identity of full alignment: 58 %
Average coverage of the sequence by the domain: 91.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.5 27.0
Noise cut-off 20.5 18.1
Model length: 46
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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 Sda domain has been found. There are 4 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.

Loading structure mapping...