Summary: Pentapeptide repeats (9 copies)
This is the Wikipedia entry entitled "Pentapeptide repeat". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Pentapeptide repeat Edit Wikipedia article
Structure of the pentapeptide repeat protein HetL.
Pentapeptide repeats are a family of sequence motifs found in multiple tandem copies in protein molecules. Pentapeptide repeat proteins are found in all species, but they are found in many copies in cyanobacterial genomes. The repeats were first identified by Black and colleagues in the hglK protein. The later Bateman et al. showed that a large family of related pentapeptide repeat proteins existed. The function of these repeats is uncertain in most proteins. However, in the MfpA protein a DNA gyrase inhibitor it has been suggested that the pentapeptide repeat structure mimics the structure of DNA. The repeats form a regular right handed four sided beta helix structure known as the Rfr-fold.
The pentapeptide repeat is a feature seen in protein sequence. It can be approximately described using the 1-letter amino acid code as A(D/N)LXX, where X can be any amino acid . This repeating sequence can be seen in multiple sequence alignments and dot plots of proteins such as HglK. The central position in the pentapeptide repeat is usually a leucine and has been designated as position i. The two previous positions are known as i-1 and i-2. Position i-2 is usually an alanine. The two subsequent positions are denoted i+1 and i+2. The side chains of positions i-2 and i point into the hydrophobic interior of the protein while the side chains of positions i-1, i+1 and i+2 are exposed on the surface of the proteins.
Pentapeptide repeats were initially predicted from sequence to possess a right handed beta helix with three sides.  The first crystal structure of a pentapeptide repeat protein was the MfpA protein solved by Hegde and colleagues. It showed that pentapeptide repeat proteins (PRPs) possessed a four sided beta helix structure. Four repeats make up one turn of a solenoid like structure. The structures of eight different proteins have been solved to date.
|Protein||PDB code||Length||Number of repeats||Reference|
|Mycobacterium tuberculosis MfpA||PDB 2bm4||183||30|||
|Cyanobacterium nostoc HetL||PDB 3du1||237||40|||
|Enterococcus faecalis EfsQnr||PDB 2w7z||211|||
|Nostoc punctiforme Np275||PDB 2J8I||98||17|||
|Nostoc punctiforme Np276||PDB 2J8K||75||12|||
|Cyanothece sp. Rfr32||PDB 2F3L PDB 2G0Y||167||21|||
|Cyanothece sp. Rfr23||PDB 2O6W||174||23|||
|Arabidopsis thaliana At2g44920||PDB 3N90||224||25|||
- Ni S, Sheldrick GM, Benning MM, Kennedy MA (January 2009). "The 2 Ã… resolution crystal structure of HetL, a pentapeptide repeat protein involved in regulation of heterocyst differentiation in the cyanobacterium Nostoc sp. strain PCC 7120". J. Struct. Biol. 165 (1): 47â€“52. doi:10.1016/j.jsb.2008.09.010. PMID 18952182.
- Vetting MW, Hegde SS, Fajardo JE et al. (January 2006). "Pentapeptide repeat proteins". Biochemistry 45 (1): 1â€“10. doi:10.1021/bi052130w. PMC 2566302. PMID 16388575.
- Bateman A, Murzin AG, Teichmann SA (June 1998). "Structure and distribution of pentapeptide repeats in bacteria". Protein Sci. 7 (6): 1477â€“80. doi:10.1002/pro.5560070625. PMC 2144021. PMID 9655353.
- Black K, Buikema WJ, Haselkorn R (November 1995). "The hglK gene is required for localization of heterocyst-specific glycolipids in the cyanobacterium Anabaena sp. strain PCC 7120". J. Bacteriol. 177 (22): 6440â€“8. PMC 177493. PMID 7592418.
- Hegde SS, Vetting MW, Roderick SL et al. (June 2005). "A fluoroquinolone resistance protein from Mycobacterium tuberculosis that mimics DNA". Science 308 (5727): 1480â€“3. doi:10.1126/science.1110699. PMID 15933203.
- Vetting MW, Hegde SS, Blanchard JS (May 2009). "Crystallization of a pentapeptide-repeat protein by reductive cyclic pentylation of free amines with glutaraldehyde". Acta Crystallogr. D Biol. Crystallogr. 65 (Pt 5): 462â€“9. doi:10.1107/S0907444909008324. PMC 2672816. PMID 19390151.
- Vetting MW, Hegde SS, Hazleton KZ, Blanchard JS (April 2007). "Structural characterization of the fusion of two pentapeptide repeat proteins, Np275 and Np276, from Nostoc punctiforme: resurrection of an ancestral protein". Protein Sci. 16 (4): 755â€“60. doi:10.1110/ps.062637707. PMC 2203339. PMID 17384236.
- Buchko GW, Ni S, Robinson H, Welsh EA, Pakrasi HB, Kennedy MA (November 2006). "Characterization of two potentially universal turn motifs that shape the repeated five-residues fold--crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142". Protein Sci. 15 (11): 2579â€“95. doi:10.1110/ps.062407506. PMC 2242410. PMID 17075135.
- Buchko GW, Robinson H, Pakrasi HB, Kennedy MA (April 2008). "Insights into the structural variation between pentapeptide repeat proteins--crystal structure of Rfr23 from Cyanothece 51142". J. Struct. Biol. 162 (1): 184â€“92. doi:10.1016/j.jsb.2007.11.008. PMID 18158251.
- Ni S, McGookey ME, Tinch SL et al. (December 2011). "The 1.7 Ã… resolution structure of At2g44920, a pentapeptide-repeat protein in the thylakoid lumen of Arabidopsis thaliana". Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67 (Pt 12): 1480â€“4. doi:10.1107/S1744309111037432. PMID 22139148.
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.
Pentapeptide repeats (9 copies) Provide feedback
No Pfam abstract.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001646These repeats were first identified in many cyanobacterial proteins but they are also found in bacterial as well as in plant proteins [PUBMED:9654141]. The repeats were first identified in hglK [PUBMED:7592418]. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix [PUBMED:9655353]. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid.
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
This clan includes proteins that form a four sided parallel beta helix. They are generally compoased of pentapeptide repeat motifs.
The clan contains the following 3 members:Pentapeptide Pentapeptide_3 Pentapeptide_4
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||45|
|Number in full:||22328|
|Average length of the domain:||78.10 aa|
|Average identity of full alignment:||16 %|
|Average coverage of the sequence by the domain:||33.74 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There are 4 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Pentapeptide_4 domain has been found. There are 53 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...