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191  structures 4760  species 2  interactions 30295  sequences 226  architectures

Family: Rhodanese (PF00581)

Summary: Rhodanese-like domain

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This is the Wikipedia entry entitled "Rhodanese". More...

Rhodanese Edit Wikipedia article

Rhodanese-like domain
Rhodanase.png
Identifiers
Symbol Rhodanese
Pfam PF00581
InterPro IPR001763
PROSITE PDOC00322
SCOP 2ora
SUPERFAMILY 2ora

Rhodanese is a mitochondrial enzyme that detoxifies cyanide (CN-) by converting it to thiocyanate (SCN-).[1]

This reaction takes place in two steps. The diagram on the right shows the crystallographically-determined structure of rhodanese. In the first step, thiosulfate reacts with the thiol group on Cysteine-247 1, to form a disulfide 2. In the second step, the disulfide reacts with cyanide to produce thiocyanate, itself being converted back into the "normal" thiol 1.

Rhodanase2.png

This reaction is important for the decontamination of cyanide, since the thiocyanate formed is relatively harmless. The use of thiosulfate solution as an antidote for cyanide poisoning is based on the activation of this enzymatic cycle.

Rhodanese shares evolutionary relationship with a large family of proteins, including

  • Cdc25 phosphatase catalytic domain.
  • non-catalytic domains of eukaryotic dual-specificity MAPK-phosphatases
  • non-catalytic domains of yeast PTP-type MAPK-phosphatases
  • non-catalytic domains of yeast Ubp4, Ubp5, Ubp7
  • non-catalytic domains of mammalian Ubp-Y
  • Drosophila heat shock protein HSP-67BB
  • several bacterial cold-shock and phage shock proteins
  • plant senescence associated proteins
  • catalytic and non-catalytic domains of rhodanese (see <db_xref db="INTERPRO" dbkey="IPR001307" />).

Rhodanese has an internal duplication. This domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.[2]

[edit] Human proteins containing this domain

CDC25A; CDC25B; CDC25C; DUSP; DUSP1; DUSP10; DUSP16; DUSP2; DUSP4; DUSP5; DUSP6; DUSP7; KAT; MKP7; MOCS3; MPST; TBCK; TSGA14; TST; USP8;

[edit] References

  1. ^ Cipollone R, Ascenzi P, Tomao P, Imperi F, Visca P (2008). "Enzymatic detoxification of cyanide: clues from Pseudomonas aeruginosa Rhodanese". J. Mol. Microbiol. Biotechnol. 15 (2-3): 199–211. doi:10.1159/000121331. PMID 18685272.
  2. ^ Gliubich F, Gazerro M, Zanotti G, Delbono S, Bombieri G, Berni R (1996). "Active site structural features for chemically modified forms of rhodanese". J. Biol. Chem. 271 (35): 21054–21061. doi:10.1074/jbc.271.35.21054. PMID 8702871.

[edit] External links

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.

Rhodanese-like domain Provide feedback

Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.

Literature references

  1. Gliubich F, Gazerro M, Zanotti G, Delbono S, Bombieri G, Berni R; , J Biol Chem 1996;271:21054-21061.: Active site structural features for chemically modified forms of rhodanese. PUBMED:8702871 EPMC:8702871


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001763

Rhodanese, a sulphurtransferase involved in cyanide detoxification (see INTERPRO) shares evolutionary relationship with a large family of proteins [PUBMED:9733650], including

  • Cdc25 phosphatase catalytic domain.
  • non-catalytic domains of eukaryotic dual-specificity MAPK-phosphatases.
  • non-catalytic domains of yeast PTP-type MAPK-phosphatases.
  • non-catalytic domains of yeast Ubp4, Ubp5, Ubp7.
  • non-catalytic domains of mammalian Ubp-Y.
  • Drosophila heat shock protein HSP-67BB.
  • several bacterial cold-shock and phage shock proteins.
  • plant senescence associated proteins.
  • catalytic and non-catalytic domains of rhodanese (see INTERPRO).

Rhodanese has an internal duplication. This domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases [PUBMED:8702871].

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
(147)
Full
(30295)
Representative proteomes NCBI
(22860)
Meta
(9896)
RP15
(2977)
RP35
(5838)
RP55
(7876)
RP75
(9427)
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Format an alignment

  Seed
(147)
Full
(30295)
Representative proteomes NCBI
(22860)
Meta
(9896)
RP15
(2977)
RP35
(5838)
RP55
(7876)
RP75
(9427)
Alignment:
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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
(147)
Full
(30295)
Representative proteomes NCBI
(22860)
Meta
(9896)
RP15
(2977)
RP35
(5838)
RP55
(7876)
RP75
(9427)
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

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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

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Curation View help on the curation process

Seed source: MRC-LMB Genome group
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 147
Number in full: 30295
Average length of the domain: 101.90 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 44.29 %

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 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 113
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Rhodanese DUF1930

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 Rhodanese domain has been found. There are 191 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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