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57  structures 2008  species 0  interactions 6775  sequences 256  architectures

Family: Pentapeptide_4 (PF13599)

Summary: Pentapeptide repeats (9 copies)

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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
Symbol Pentapeptide
Pfam PF00805
InterPro IPR001646

Pentapeptide repeats are a family of sequence motifs found in multiple tandem copies in protein molecules.[2][3] 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.[4] The later Bateman et al. showed that a large family of related pentapeptide repeat proteins existed.[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.[5] The repeats form a regular right handed four sided beta helix structure known as the Rfr-fold.


Sequence features

Multiple sequence alignment of pentapeptide repeat proteins.
Dot plot of the HglK protein against itself showing repeats as diagonal lines.

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.


Structure

Pentapeptide repeats were initially predicted from sequence to possess a right handed beta helix with three sides. [3] 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.[5] 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 [5]
Cyanobacterium nostoc HetL PDB 3du1 237 40 [1]
Enterococcus faecalis EfsQnr PDB 2w7z 211 [6]
Nostoc punctiforme Np275 PDB 2J8I 98 17 [7]
Nostoc punctiforme Np276 PDB 2J8K 75 12 [7]
Cyanothece sp. Rfr32 PDB 2F3L PDB 2G0Y 167 21 [8]
Cyanothece sp. Rfr23 PDB 2O6W 174 23 [9]
Arabidopsis thaliana At2g44920 PDB 3N90 224 25 [10]



References

  1. ^ a b 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. 
  2. ^ Vetting MW, Hegde SS, Fajardo JE, et al. (January 2006). "Pentapeptide repeat proteins". Biochemistry 45 (1): 1–10. doi:10.1021/bi052130w. PMC 2566302. PMID 16388575. 
  3. ^ a b c 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 2144021. PMID 9655353. 
  4. ^ 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 177493. PMID 7592418. 
  5. ^ a b c 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. 
  6. ^ 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): 462–9. doi:10.1107/S0907444909008324. PMC 2672816. PMID 19390151. 
  7. ^ a b 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 2203339. PMID 17384236. 
  8. ^ 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 2242410. PMID 17075135. 
  9. ^ 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. 
  10. ^ 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 (9 copies) Provide feedback

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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


External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

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

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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.

  Seed
(86)
Full
(6775)
Representative proteomes NCBI
(10345)
Meta
(2693)
RP15
(562)
RP35
(1041)
RP55
(1333)
RP75
(1619)
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Format an alignment

  Seed
(86)
Full
(6775)
Representative proteomes NCBI
(10345)
Meta
(2693)
RP15
(562)
RP35
(1041)
RP55
(1333)
RP75
(1619)
Alignment:
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Order:
Sequence:
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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
(86)
Full
(6775)
Representative proteomes NCBI
(10345)
Meta
(2693)
RP15
(562)
RP35
(1041)
RP55
(1333)
RP75
(1619)
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.

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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
Author: Coggill P
Number in seed: 86
Number in full: 6775
Average length of the domain: 77.40 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 36.50 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 78
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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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 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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