RHODRhodanese 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 has an internal duplication. This domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases [(PUBMED:8702871)].
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- 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)
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% 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) 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 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 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
- Links (links to other resources describing this domain)