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4  structures 183  species 1  interaction 280  sequences 7  architectures

Family: Phytochelatin (PF05023)

Summary: Phytochelatin synthase

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Phytochelatin synthase Provide feedback

Phytochelatin synthase is the enzyme responsible for the synthesis of heavy-metal-binding peptides (phytochelatins) from glutathione and related thiols [2]. The crystal structure of a member of this family shows it to possess a papain fold [3]. The enzyme catalyses the deglycination of a GSH donor molecule [3]. The enzyme contains a catalytic triad of cysteine, histidine and aspartate residues.

Literature references

  1. Clemens S, Kim EJ, Neumann D, Schroeder JI; , EMBO J 1999;18:3325-3333.: Tolerance to toxic metals by a gene family of phytochelatin synthases from plants and yeast. PUBMED:10369673 EPMC:10369673

  2. Vatamaniuk OK, Bucher EA, Ward JT, Rea PA; , Trends Biotechnol 2002;20:61-64.: Worms take the 'phyto' out of 'phytochelatins'. PUBMED:11814595 EPMC:11814595

  3. Vivares D, Arnoux P, Pignol D; , Proc Natl Acad Sci U S A. 2005;102:18848-18853.: A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis. PUBMED:16339904 EPMC:16339904


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007719

This entry represents plant phytochelatin synthases (also known as glutathione gamma-glutamylcysteinyltransferase; EC), which is involved in the synthesis of phytochelatins (PC) and homophytochelatins (hPC), the heavy-metal-binding peptides of plants. This enzyme is required for detoxification of heavy metals such as cadmium and arsenate. The N-terminal region of phytochelatin synthase contains the active site, as well as four highly conserved cysteine residues that appear to play an important role in heavy-metal-induced phytochelatin catalysis. The C-terminal region is rich in cysteines, and may act as a metal sensor, whereby the Cys residues bind cadmium ions to bring them into closer proximity and transferring them to the activation site in the N-terminal catalytic domain [PUBMED:18270423]. The C-terminal region displays homology to the functional domains of metallothionein and metallochaperone.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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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
(20)
Full
(280)
Representative proteomes NCBI
(295)
Meta
(16)
RP15
(64)
RP35
(91)
RP55
(107)
RP75
(123)
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Format an alignment

  Seed
(20)
Full
(280)
Representative proteomes NCBI
(295)
Meta
(16)
RP15
(64)
RP35
(91)
RP55
(107)
RP75
(123)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(20)
Full
(280)
Representative proteomes NCBI
(295)
Meta
(16)
RP15
(64)
RP35
(91)
RP55
(107)
RP75
(123)
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.

Pfam alignments:

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: Pfam-B_9299 (release 7.6)
Previous IDs: none
Type: Domain
Author: Wood V, Rawlings ND
Number in seed: 20
Number in full: 280
Average length of the domain: 197.80 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 55.01 %

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 23.8 23.8
Trusted cut-off 23.8 24.0
Noise cut-off 23.4 23.7
Model length: 213
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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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 adjacent tab. More...

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Interactions

There is 1 interaction for this family. More...

Phytochelatin

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 Phytochelatin 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.

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