Summary: Pentapeptide repeats (8 copies)
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This is the Wikipedia entry entitled "Pentapeptide repeat". More...
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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||||183||30|||
|Cyanobacterium nostoc HetL||||237||40|||
|Enterococcus faecalis EfsQnr||||211|||
|Nostoc punctiforme Np275||||98||17|||
|Nostoc punctiforme Np276||||75||12|||
|Cyanothece sp. Rfr32|| ||167||21|||
|Cyanothece sp. Rfr23||||174||23|||
|Arabidopsis thaliana At2g44920||||224||25|||
- Ni S, Sheldrick GM, Benning MM, Kennedy MA (January 2009). "The 2 Å 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): 47–52. 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): 1–10. doi:10.1021/bi052130w. PMC . PMID 16388575.
- Bateman A, Murzin AG, Teichmann SA (June 1998). "Structure and distribution of pentapeptide repeats in bacteria". Protein Sci. 7 (6): 1477–80. doi:10.1002/pro.5560070625. PMC . 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): 6440–8. PMC . 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): 1480–3. 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. 65 (Pt 5): 462–9. doi:10.1107/S0907444909008324. PMC . 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): 755–60. doi:10.1110/ps.062637707. PMC . 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): 2579–95. doi:10.1110/ps.062407506. PMC . 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): 184–92. doi:10.1016/j.jsb.2007.11.008. PMID 18158251.
- Ni S, McGookey ME, Tinch SL, et al. (December 2011). "The 1.7 Å 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): 1480–4. doi:10.1107/S1744309111037432. PMID 22139148.
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Pentapeptide repeats (8 copies) Provide feedback
These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK . The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix . The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid.
Black K, Buikema WJ, Haselkorn R; , J Bacteriol 1995;177:6440-6448.: The hglK gene is required for localization of heterocyst-specific glycolipids in the cyanobacterium Anabaena sp. strain PCC 7120. PUBMED:7592418 EPMC:7592418
Kieselbach T, Mant A, Robinson C, Schroder WP; , FEBS Lett 1998;428:241-244.: Characterisation of an Arabidopsis cDNA encoding a thylakoid lumen protein related to a novel 'pentapeptide repeat' family of proteins. PUBMED:9654141 EPMC:9654141
Internal database links
|Similarity to PfamA using HHSearch:||Pentapeptide_3 Pentapeptide_3|
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.
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- 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
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
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Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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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 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...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
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 UniProtKB sequence database using the family HMM
- 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:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
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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.
|Seed source:||Bateman A|
|Number in seed:||184|
|Number in full:||21308|
|Average length of the domain:||37.80 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||32.86 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||21|
|Download:||download the raw HMM for this family|
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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 More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
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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 domain has been found. There are 57 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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