Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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RHOD Rhodanese Homology Domain

SMART accession number:	SM00450
Description:	An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.
Interpro abstract (IPR001763):	Rhodanese, a sulphurtransferase involved in cyanide detoxification (see IPR001307 ) 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 IPR001307 ). 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) ].
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 171652 RHOD domains in 136038 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing RHOD domain.

  This tree includes only several representative species. The complete taxonomic breakdown of all proteins with RHOD domain is also avaliable.

  Click on the protein counts, or double click on taxonomic names to display all proteins containing RHOD domain in the selected taxonomic class.

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Hofmann K, Bucher P, Kajava AV
  • A model of Cdc25 phosphatase catalytic domain and Cdk-interaction surface based on the presence of a rhodanese homology domain.
  • J Mol Biol. 1998; 282: 195-208
  • Display abstract

  • Mammalian Cdc25 phosphatase is responsible for the dephosphorylation of Cdc2 and other cyclin-dependent kinases at Thr14 and Tyr15, thus activating the kinase and allowing cell cycle progression. The catalytic domain of this dual-specificity phosphatase has recently been mapped to the 180 most C-terminal amino acids. Apart from a CX3R motif, which is present at the active site of all known tyrosine phosphatases, Cdc25 does not share any obvious sequence similarity with any of those enzymes. Until very recently, the Cdc25 family was the only subfamily of tyrosine phosphates for which no three-dimensional structural data were available. Using the generalized profile technique, a sensitive method for sequence database searches, we found an extended and highly significant sequence similarity between the Cdc25 catalytic domain and similarly sized regions in other proteins: the non-catalytic domain of two distinct families of MAP-kinase phosphates, the non-catalytic domain of several ubiquitin protein hydrolases, the N and C-terminal domain of rhodanese, and a large and heterogeneous groups of stress-response proteins from all phyla. The relationship of Cdc25 to the structurally well-characterized rhodanese spans the entire catalytic domain and served as template for a structural model for human Cdc25a, which is fundamentally different from previously suggested models for Cdc25 catalytic domain organization. The surface positioning of subfamily-specific conserved residues allows us to predict the sites of interaction with Cdk2, a physiological target of Cdc25a. Based on the results of this analysis, we also predict that the budding yeast arsenate resistance protein Acr2 and the ORF Ygr203w encode protein phosphatases with catalytic properties similar to that of the Cdc25 family. Recent determination of the crystal structure of the Cdc25a catalytic domain supports the validity of the model and demonstrates the power of the generalized sequence profile technique in homology-based modeling of the three-dimensional structure of a protein having a weak but significant sequence similarity with a structurally characterized protein.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 29.39 map00272 Cysteine metabolism 26.34 map04010 MAPK signaling pathway 9.54 map00790 Folate biosynthesis 8.40 map00620 Pyruvate metabolism 5.73 map04110 Cell cycle 5.73 map04914 Progesterone-mediated oocyte maturation 3.44 map00190 Oxidative phosphorylation 3.05 map00730 Thiamine metabolism 1.91 map04111 Cell cycle - yeast 1.15 map00260 Glycine, serine and threonine metabolism 1.15 map00910 Nitrogen metabolism 1.15 map00564 Glycerophospholipid metabolism 0.76 map00450 Selenoamino acid metabolism 0.76 map00920 Sulfur metabolism 0.38 map00252 Alanine and aspartate metabolism 0.38 map00500 Starch and sucrose metabolism 0.38 map00460 Cyanoamino acid metabolism 0.38 map00271 Methionine metabolism This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with RHOD domain which could be assigned to a KEGG orthologous group, and not all proteins containing RHOD domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of RHOD domains in PDB

  PDB code	Main view	Title
  1boh		SULFUR-SUBSTITUTED RHODANESE (ORTHORHOMBIC FORM)
  1boi		N-TERMINALLY TRUNCATED RHODANESE
  1c25		HUMAN CDC25A CATALYTIC DOMAIN
  1cwr		HUMAN CDC25B CATALYTIC DOMAIN WITHOUT ION IN CATALYTIC SITE
  1cws		HUMAN CDC25B CATALYTIC DOMAIN WITH TUNGSTATE
  1cwt		HUMAN CDC25B CATALYTIC DOMAIN WITH METHYL MERCURY
  1dp2		CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RHODANESE AND LIPOATE
  1e0c		SULFURTRANSFERASE FROM AZOTOBACTER VINELANDII
  1gmx		Escherichia coli GlpE sulfurtransferase
  1gn0		Escherichia coli GlpE sulfurtransferase soaked with KCN
  1h4k		Sulfurtransferase from Azotobacter vinelandii in complex with hypophosphite
  1h4m		Sulfurtransferase from Azotobacter vinelandii in complex with phosphate
  1hzm		STRUCTURE OF ERK2 BINDING DOMAIN OF MAPK PHOSPHATASE MKP-3: STRUCTURAL INSIGHTS INTO MKP-3 ACTIVATION BY ERK2
  1okg		3-mercaptopyruvate sulfurtransferase from Leishmania major
  1orb		ACTIVE SITE STRUCTURAL FEATURES FOR CHEMICALLY MODIFIED FORMS OF RHODANESE
  1qb0		HUMAN CDC25B CATALYTIC DOMAIN
  1qxn		Solution Structure of the 30 kDa Polysulfide-sulfur Transferase Homodimer from Wolinella Succinogenes
  1rhd		STRUCTURE OF BOVINE LIVER RHODANESE. I. STRUCTURE DETERMINATION AT 2.5 ANGSTROMS RESOLUTION AND A COMPARISON OF THE CONFORMATION AND SEQUENCE OF ITS TWO DOMAINS
  1rhs		SULFUR-SUBSTITUTED RHODANESE
  1t3k		NMR structure of a CDC25-like dual-specificity tyrosine phosphatase of Arabidopsis thaliana
  1tq1		Solution structure of At5g66040, a putative protein from Arabidosis Thaliana
  1uar		Crystal structure of Rhodanese from Thermus thermophilus HB8
  1urh		The ""Rhodanese"" fold and catalytic mechanism of 3-mercaptopyruvate sulfotransferases: Crystal structure of SseA from Escherichia coli
  1whb		Solution structure of the Rhodanese-like domain in human ubiquitin specific protease 8 (UBP8)
  1wv9		Crystal Structure of Rhodanese Homolog TT1651 from an Extremely Thermophilic Bacterium Thermus thermophilus HB8
  1ym9		Crystal structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfinic form
  1ymd		Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfonic form
  1ymk		Crystal Structure of the CDC25B phosphatase catalytic domain in the apo form
  1yml		Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfenic form
  1ys0		Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the disulfide form
  1yt8		Crystal Structure of Thiosulfate sulfurtransferase from Pseudomonas aeruginosa
  2a2k		Crystal Structure of an active site mutant, C473S, of Cdc25B Phosphatase Catalytic Domain
  2eg3		Crystal Structure of Probable Thiosulfate Sulfurtransferase
  2eg4		Crystal Structure of Probable Thiosulfate Sulfurtransferase
  2fsx		Crystal structure of Rv0390 from M. tuberculosis
  2gwf		Structure of a USP8-NRDP1 complex
  2hhg		Structure of Protein of Unknown Function RPA3614, Possible Tyrosine Phosphatase, from Rhodopseudomonas palustris CGA009
  2ifd		Crystal structure of a remote binding site mutant, R492L, of CDC25B Phosphatase catalytic domain
  2ifv		Crystal structure of an active site mutant, C473D, of CDC25B phosphatase catalytic domain
  2j6p		Structure of As-Sb reductase from Leishmania major
  2jtq		Rhodanese from E.coli
  2jtr		rhodanese persulfide from E. coli
  2jts		rhodanese with anions from E. coli
  2k0z		Solution NMR structure of protein hp1203 from Helicobacter pylori 26695. Northeast Structural Genomics Consortium (NESG) target PT1/Ontario Center for Structural Proteomics target hp1203
  2kl3		Solution NMR structure of the Rhodanese-like domain from Anabaena sp Alr3790 protein. Northeast Structural Genomics Consortium Target NsR437A
  2moi		2MOI
  2mol		2MOL
  2mrm		2MRM
  2ora		RHODANESE (THIOSULFATE: CYANIDE SULFURTRANSFERASE)
  2ouc		Crystal structure of the MAP kinase binding domain of MKP5
  2uzq		Protein Phosphatase, New Crystal Form
  2vsw		The structure of the rhodanese domain of the human dual specificity phosphatase 16
  2wlr		Putative thiosulfate sulfurtransferase YnjE
  2wlx		Putative thiosulfate sulfurtransferase YnjE
  3aax		Crystal structure of probable thiosulfate sulfurtransferase cysa3 (RV3117) from Mycobacterium tuberculosis: monoclinic FORM
  3aay		Crystal structure of probable thiosulfate sulfurtransferase CYSA3 (RV3117) from Mycobacterium tuberculosis: orthorhombic form
  3d1p		Atomic resolution structure of uncharacterized protein from Saccharomyces cerevisiae
  3dtt		Crystal structure of a putative f420 dependent nadp-reductase (arth_0613) from arthrobacter sp. fb24 at 1.70 A resolution
  3f4a		Structure of Ygr203w, a yeast protein tyrosine phosphatase of the Rhodanese family
  3flh		Crystal structure of lp_1913 protein from Lactobacillus plantarum,Northeast Structural Genomics Consortium Target LpR140B
  3fnj		Crystal structure of the full-length lp_1913 protein from Lactobacillus plantarum, Northeast Structural Genomics Consortium Target LpR140
  3foj		Crystal Structure of SSP1007 From Staphylococcus saprophyticus subsp. saprophyticus. Northeast Structural Genomics Target SyR101A.
  3fs5		Crystal structure of Saccharomyces cerevisiae Ygr203w, a homolog of single-domain rhodanese and Cdc25 phosphatase catalytic domain
  3g5j		Crystal structure of N-terminal domain of putative ATP/GTP binding protein from Clostridium difficile 630
  3gk5		Crystal structure of rhodanese-related protein (TVG0868615) from Thermoplasma volcanium, Northeast Structural Genomics Consortium Target TvR109A
  3hix		Crystal Structure of the Rhodanese_3 like domain from Anabaena sp Alr3790 protein. Northeast Structural Genomics Consortium Target NsR437i
  3hwi		Crystal structure of probable thiosulfate sulfurtransferase Cysa2 (Rhodanese-like protein) from Mycobacterium tuberculosis
  3hzu		Crystal structure of probable thiosulfate sulfurtransferase SSEA (rhodanese) from Mycobacterium tuberculosis
  3i2v		Crystal structure of human MOCS3 rhodanese-like domain
  3i3u		Crystal structure of lp_1913 protein from lactobacillus plantarum, northeast structural genomics Consortium target lpr140a
  3icr		Crystal structure of oxidized Bacillus anthracis CoADR-RHD
  3ics		Crystal structure of partially reduced Bacillus anthracis CoADR-RHD
  3ict		Crystal structure of reduced Bacillus anthracis CoADR-RHD
  3ilm		Crystal Structure of the Alr3790 protein from Anabaena sp. Northeast Structural Genomics Consortium Target NsR437h
  3ipo		Crystal structure of YnjE
  3ipp		crystal structure of sulfur-free YnjE
  3iwh		Crystal Structure of Rhodanese-like Domain Protein from Staphylococcus aureus
  3k9r		X-ray structure of the Rhodanese-like domain of the Alr3790 protein from Anabaena sp. Northeast Structural Genomics Consortium Target NsR437c.
  3mzz		Crystal Structure of Rhodanese-like Domain Protein from Staphylococcus aureus
  3nhv		Crystal Structure of BH2092 protein from Bacillus halodurans, Northeast Structural Genomics Consortium Target BhR228F
  3nt6		Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase C43S/C531S Double Mutant
  3nta		Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase
  3ntd		Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase C531S Mutant
  3o3w		Crystal Structure of BH2092 protein (residues 14-131) from Bacillus halodurans, Northeast Structural Genomics Consortium Target BhR228A
  3olh		Human 3-mercaptopyruvate sulfurtransferase
  3op3		Crystal Structure of Cell Division Cycle 25C Protein Isoform A from Homo sapiens
  3p3a		Crystal structure of a putative thiosulfate sulfurtransferase from Mycobacterium thermoresistible
  3r2u		2.1 Angstrom Resolution Crystal Structure of Metallo-beta-lactamase from Staphylococcus aureus subsp. aureus COL
  3tg1		Crystal structure of p38alpha in complex with a MAPK docking partner
  3tg3		Crystal structure of the MAPK binding domain of MKP7
  3tp9		Crystal structure of Alicyclobacillus acidocaldarius protein with beta-lactamase and rhodanese domains
  3utn		Crystal structure of Tum1 protein from Saccharomyces cerevisiae
  4f67		Three dimensional structure of the double mutant of UPF0176 protein lpg2838 from Legionella pneumophila at the resolution 1.8A, Northeast Structural Genomics Consortium (NESG) Target LgR82
  4jgt		Structure and kinetic analysis of H2S production by human Mercaptopyruvate Sulfurtransferase
  4ocg		4OCG
  4wh7		4WH7
  4wh9		4WH9
  5hbl		5HBL
  5hbo		5HBO
  5hbp		5HBP
  5hbq		5HBQ
  5lam		5LAM
  5lao		5LAO

• Links (links to other resources describing this domain)

• INTERPRO	IPR001763

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