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.
74  structures 3420  species 0  interactions 9344  sequences 432  architectures

Family: Pentapeptide_4 (PF13599)

Summary: Pentapeptide repeats (9 copies)

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 "Pentapeptide repeat". More...

Pentapeptide repeat Edit Wikipedia article

Pentapeptide repeat
PDB 3du1 EBI.png
Structure of the pentapeptide repeat protein HetL.[1]
Identifiers
SymbolPentapeptide
PfamPF00805
InterProIPR001646

Pentapeptide repeats are a family of sequence motifs found in protein molecules.[2] These repeats are found in many cyanobacterial proteins, but do occur in many other bacteria. The repeats were first identified in the hglK protein.[3] 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.[4] The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid using the 1-letter amino acid code. The repeats form a regular right handed four sided beta helix structure.

References

  1. ^ Ni S, Sheldrick GM, Benning MM, Kennedy MA (2009). "The 2A 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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Bateman A, Murzin AG, Teichmann SA (1998). "Structure and distribution of pentapeptide repeats in bacteria". Protein Sci. 7 (6): 1477–80. doi:10.1002/pro.5560070625. PMC 2144021. PMID 9655353. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ Black K, Buikema WJ, Haselkorn R (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 177493. PMID 7592418. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  4. ^ Hegde SS, Vetting MW, Roderick SL; et al. (2005). "A fluoroquinolone resistance protein from Mycobacterium tuberculosis that mimics DNA". Science. 308 (5727): 1480–3. doi:10.1126/science.1110699. PMID 15933203. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

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.

Pentapeptide repeats (9 copies) Provide feedback

No Pfam abstract.

Literature references

  1. Bateman A, Murzin A, Teichmann SA; , Protein Sci 1998;7:1477-1480.: Structure and distribution of pentapeptide repeats in bacteria. PUBMED:9655353 EPMC:9655353


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001646

These 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 ]. Pentapeptide repeat proteins (PRPs) are characterised by the repetition of the pentapeptide repeat motif [S,T,A,V][D,N][L,F][S,T,R][G], which allows it to adopt a right-handed beta-helical structure conformation [ PUBMED:9655353 ]. The functions of these repeats is unknown but it has been shown that members of this family share the ability to interact with DNA-binding proteins, such as DNA gyrase. For example, McbG (from Escherichia coli) protects the DNA gyrase from microcin B17 toxicity, MfpAMt (from Mycobacterium tuberculosis) and Qnr (from Klebsiella pneumoniae and other enterobacteria) are involved in resistance to fluoroquinolones [ PUBMED:19060136 ].

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 Pentapeptide (CL0505), which has the following description:

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

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
(20)
Full
(9344)
Representative proteomes UniProt
(42376)
RP15
(1097)
RP35
(4176)
RP55
(9501)
RP75
(17439)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(20)
Full
(9344)
Representative proteomes UniProt
(42376)
RP15
(1097)
RP35
(4176)
RP55
(9501)
RP75
(17439)
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
(20)
Full
(9344)
Representative proteomes UniProt
(42376)
RP15
(1097)
RP35
(4176)
RP55
(9501)
RP75
(17439)
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: Jackhmmer:C2M218
Previous IDs: none
Type: Repeat
Sequence Ontology: SO:0001068
Author: Coggill P
Number in seed: 20
Number in full: 9344
Average length of the domain: 74.8 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 35.79 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 78
Family (HMM) version: 9
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 Pentapeptide_4 domain has been found. There are 74 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...