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.
298  structures 8602  species 0  interactions 77917  sequences 571  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

thumb|300px|Abb. 1.Tertiärstruktur der Rhodanase mit persulfidiertem Cystein-247-Rest im katalytischen Zentrum.

' the ' Rhodanase ' ' ' (also Rhodanese, Thiosulfat Sulfurtransferase, Thiosulfat cyanide Transsulfurase; [ [ EC Nummer|EC ] ] [ http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/8/1/1.html 2.8.1.1 ]) is [ [ Mitochondrium|mitochondriales ] ] [ [ enzyme ] ], which sulfur of [ [ Thiosulfat ] ] (S 2 O 3 -2) on [ [ cyanide ] ] (CN -) transfers. Thus the latter becomes [ [ Rhodanid ] ] (Thiocyanat, SCN -), while the Thiosulfat to [ [ sulfite ] ] (SO 3 -2) one reduces.

This reaction takes place in two steps. The Abb. 1 shows the radiographically determined structure of the Rhodanase. Therein one can recognize a disulfidische connection in the catalytic center of the enzyme very well. This is formed in the first step, by a Schwefeldonor, here Thiosulfat, its sulfur on [ [ Thiol]] group [ [ Cystein]]s-247-Restes ' ' ' 1 ' ' ' under education [ [ Disulfan]]s ' ' ' 2 ' ' ' transfers. In the second step under recovery of the "normal" Thiol group the substrate, here cyanide, is sulfidiert:

[ [ Bild:Rhodanase2.png ] ]

This reaction is important for the decontamination of taken up cyanide, since the developing Thiocyanat is as far as possible innocuous. The administration of Thiosulfat (e.g. in form of one [ [ Natriumthiosulfat]] solution) with cyanide poisonings is based also on the activation of this enzymatic decontamination system. Vordergruendig seems to be this reaction the actual task of the Rhodanase; over its actual meaning so far no clarity prevails. A role as Schwefeldonor with the synthesis of [ [ iron sulfur Cluster]]n for [ [ iron sulfur proteins ] ] is discussed.

Literature

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...

Pfam Clan

This family is a member of clan Phosphatase (CL0031), which has the following description:

This family includes tyrosine and dual specificity phosphatase enzymes.

The clan contains the following 16 members:

BLH_phosphatase CDKN3 DSPc DSPn Init_tRNA_PT LMWPc Myotub-related NleF_casp_inhib PTPlike_phytase PTS_IIB Rhodanese Ssu72 Syja_N Y_phosphatase Y_phosphatase2 Y_phosphatase3

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
(141)
Full
(77917)
Representative proteomes UniProt
(306962)
RP15
(10453)
RP35
(35148)
RP55
(75296)
RP75
(127124)
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
(141)
Full
(77917)
Representative proteomes UniProt
(306962)
RP15
(10453)
RP35
(35148)
RP55
(75296)
RP75
(127124)
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
(141)
Full
(77917)
Representative proteomes UniProt
(306962)
RP15
(10453)
RP35
(35148)
RP55
(75296)
RP75
(127124)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 141
Number in full: 77917
Average length of the domain: 105.5 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 40.47 %

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 22.2 22.2
Trusted cut-off 22.2 22.2
Noise cut-off 22.1 22.1
Model length: 107
Family (HMM) version: 23
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 Rhodanese domain has been found. There are 298 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...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044RAJ9 View 3D Structure Click here
A0A044TFB3 View 3D Structure Click here
A0A044TKL0 View 3D Structure Click here
A0A044U8S1 View 3D Structure Click here
A0A044U8S8 View 3D Structure Click here
A0A044U8V9 View 3D Structure Click here
A0A044U8X5 View 3D Structure Click here
A0A044UDU8 View 3D Structure Click here
A0A044UHF6 View 3D Structure Click here
A0A077YXS8 View 3D Structure Click here
A0A077YZL7 View 3D Structure Click here
A0A077Z0G9 View 3D Structure Click here
A0A077Z4A6 View 3D Structure Click here
A0A077Z538 View 3D Structure Click here
A0A077Z9N1 View 3D Structure Click here
A0A077ZCR3 View 3D Structure Click here
A0A077ZDX1 View 3D Structure Click here
A0A077ZEV8 View 3D Structure Click here
A0A077ZGI4 View 3D Structure Click here
A0A077ZIC1 View 3D Structure Click here
A0A077ZJA6 View 3D Structure Click here
A0A0D2DRJ7 View 3D Structure Click here
A0A0D2EKM0 View 3D Structure Click here
A0A0D2GNM5 View 3D Structure Click here
A0A0D2H441 View 3D Structure Click here
A0A0D2H923 View 3D Structure Click here
A0A0D2HFE2 View 3D Structure Click here
A0A0G2K9Q0 View 3D Structure Click here
A0A0G2KNS1 View 3D Structure Click here
A0A0H3GRI8 View 3D Structure Click here
A0A0H3GS20 View 3D Structure Click here
A0A0H3GSL7 View 3D Structure Click here
A0A0H3GVF7 View 3D Structure Click here
A0A0H3GWP1 View 3D Structure Click here
A0A0H3GXB2 View 3D Structure Click here
A0A0H3GZB2 View 3D Structure Click here
A0A0H3GZJ5 View 3D Structure Click here
A0A0H5SKT7 View 3D Structure Click here
A0A0K0DSJ8 View 3D Structure Click here
A0A0K0DXQ5 View 3D Structure Click here