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.
204  structures 1933  species 11  interactions 14452  sequences 215  architectures

Family: Rhodanese (PF00581)

Summary: Rhodanese-like domain

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 "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, also known as rhodanase, thiosulfate sulfurtransferase, thiosulfate cyanide transsulfurase, and thiosulfate thiotransferase,[1] is a mitochondrial enzyme that detoxifies cyanide (CN) by converting it to thiocyanate (SCN).[2]

This reaction takes place in two steps. The diagram on the right shows the crystallographically-determined structure of rhodanese. In the first step, thiosulfate is reduced by the thiol group on cysteine-247 1, to form a persulfide and a sulfite 2. In the second step, the persulfide reacts with cyanide to produce thiocyanate, re-generating the cysteine thiol 1.

Rhodanase2.png

This reaction is important for the treatment of exposure to cyanide, since the thiocyanate formed is less toxic.[medical citation needed] 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.[3]

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;

Nomenclature

Although the standard nomenclature rules for enzymes indicate that their names are to end with the letters "-ase", rhodanese was first described in 1933,[4] prior to the 1955 establishment of the Enzyme Commission; as such, the older name had already attained widespread usage.

References

  1. ^ EC 2.8.1.1, at the International Union of Biochemistry and Molecular Biology
  2. ^ 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. 
  3. ^ 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. 
  4. ^ Common Themes and Variations in the Rhodanese Superfamily, by Rita Cipollone, Paolo Ascenzi, and Paolo Visca, in IUBMB Life, vol. 59, no. 2 (February 2007); page 51-59; DOI: 10.1080/15216540701206859

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


Internal database links

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...

Loading domain graphics...

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(143)
Full
(14452)
Representative proteomes UniProt
(61573)
NCBI
(92758)
Meta
(9484)
RP15
(3690)
RP35
(9310)
RP55
(14304)
RP75
(19154)
Jalview View  View  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
(143)
Full
(14452)
Representative proteomes UniProt
(61573)
NCBI
(92758)
Meta
(9484)
RP15
(3690)
RP35
(9310)
RP55
(14304)
RP75
(19154)
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
(143)
Full
(14452)
Representative proteomes UniProt
(61573)
NCBI
(92758)
Meta
(9484)
RP15
(3690)
RP35
(9310)
RP55
(14304)
RP75
(19154)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: MRC-LMB Genome group
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 143
Number in full: 14452
Average length of the domain: 105.70 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 39.19 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -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: 107
Family (HMM) version: 17
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.

Interactions

There are 11 interactions for this family. More...

USP8_interact Pyr_redox_2 Pyr_redox_dim DUF1930 Pyr_redox_2 Pyr_redox Lactamase_B Rhodanese Lactamase_B USP8_interact Pkinase

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 204 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.

Loading structure mapping...