Rhodanese/Cell cycle control phosphatase superfamily

SCOP classification

Root:	SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:	Alpha and beta proteins (a/b) [ 51349] (147)
Fold:	Rhodanese/Cell cycle control phosphatase [ 52820]
Superfamily:	Rhodanese/Cell cycle control phosphatase [ 52821] (4)
Families:	Cell cycle control phosphatase, catalytic domain [ 52822] (4)
	Single-domain sulfurtransferase [ 69509] (3)
	Multidomain sulfurtransferase (rhodanese) [ 52827] (4)
	Ubiquitin carboxyl-terminal hydrolase 8, USP8 [ 117586]

Superfamily statistics

	Genomes (2,318)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	19,766	52,310	30
Proteins	16,313	42,750	20

Functional annotation

General category	Processes_IC
Detailed category	Cell cycle, Apoptosis

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)

	GO term	FDR (singleton)	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	protein metabolic process	0.9487	3.15e-08	Least Informative	Inherited
Biological Process (BP)	cellular macromolecule metabolic process	0.9912	1.387e-05	Least Informative	Inherited
Biological Process (BP)	phosphate-containing compound metabolic process	0.2958	1.608e-09	Moderately Informative	Inherited
Biological Process (BP)	cellular protein modification process	0.4636	0	Moderately Informative	Inherited
Biological Process (BP)	dephosphorylation	6.364e-05	0	Informative	Direct
Biological Process (BP)	protein dephosphorylation	0.0005451	0	Highly Informative	Direct
Molecular Function (MF)	transferase activity	0.09541	1	Least Informative	Inherited
Molecular Function (MF)	sulfurtransferase activity	9.987e-15	0	Highly Informative	Direct

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)

	GO term	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	protein metabolic process	3.15e-08	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	1.387e-05	Least Informative	Direct
Biological Process (BP)	cellular component organization or biogenesis	1	Least Informative	Inherited
Biological Process (BP)	single-organism cellular process	1	Least Informative	Inherited
Biological Process (BP)	biosynthetic process	1	Least Informative	Inherited
Biological Process (BP)	developmental process	1	Least Informative	Inherited
Biological Process (BP)	localization	1	Least Informative	Inherited
Biological Process (BP)	regulation of cellular process	0.6841	Least Informative	Inherited
Biological Process (BP)	response to stimulus	1	Least Informative	Inherited
Biological Process (BP)	regulation of metabolic process	0.2105	Least Informative	Inherited
Biological Process (BP)	phosphate-containing compound metabolic process	1.608e-09	Moderately Informative	Direct
Biological Process (BP)	cellular protein modification process	0	Moderately Informative	Direct
Biological Process (BP)	regulation of protein metabolic process	3.947e-11	Moderately Informative	Direct
Biological Process (BP)	regulation of molecular function	1.748e-08	Moderately Informative	Direct
Biological Process (BP)	negative regulation of metabolic process	1.179e-05	Moderately Informative	Direct
Biological Process (BP)	regulation of signaling	0.0001423	Moderately Informative	Direct
Biological Process (BP)	regulation of cell communication	0.0001542	Moderately Informative	Direct
Biological Process (BP)	anatomical structure morphogenesis	0.9922	Moderately Informative	Inherited
Biological Process (BP)	cellular component biogenesis	0.5009	Moderately Informative	Inherited
Biological Process (BP)	organic substance transport	0.8186	Moderately Informative	Inherited
Biological Process (BP)	macromolecule localization	0.8508	Moderately Informative	Inherited
Biological Process (BP)	cellular localization	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of cellular metabolic process	0.08834	Moderately Informative	Inherited
Biological Process (BP)	negative regulation of cellular process	0.00327	Moderately Informative	Inherited
Biological Process (BP)	cellular response to stress	1	Moderately Informative	Inherited
Biological Process (BP)	single-organism developmental process	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of response to stimulus	0.001265	Moderately Informative	Inherited
Biological Process (BP)	signal transduction	1	Moderately Informative	Inherited
Biological Process (BP)	dephosphorylation	0	Informative	Direct
Biological Process (BP)	negative regulation of protein metabolic process	1.631e-13	Informative	Direct
Biological Process (BP)	negative regulation of signaling	6.721e-13	Informative	Direct
Biological Process (BP)	negative regulation of cell communication	9.185e-13	Informative	Direct
Biological Process (BP)	negative regulation of response to stimulus	4.242e-11	Informative	Direct
Biological Process (BP)	regulation of intracellular protein kinase cascade	2.005e-08	Informative	Direct
Biological Process (BP)	negative regulation of cellular metabolic process	1.277e-06	Informative	Direct
Biological Process (BP)	negative regulation of molecular function	4.965e-06	Informative	Direct
Biological Process (BP)	regulation of protein phosphorylation	4.484e-05	Informative	Direct
Biological Process (BP)	sulfur compound biosynthetic process	0.0007473	Informative	Direct
Biological Process (BP)	cell cycle process	0.007739	Informative	Inherited
Biological Process (BP)	regulation of kinase activity	0.006225	Informative	Inherited
Biological Process (BP)	cellular component morphogenesis	0.5868	Informative	Inherited
Biological Process (BP)	cell projection organization	0.2618	Informative	Inherited
Biological Process (BP)	anatomical structure formation involved in morphogenesis	0.1652	Informative	Inherited
Biological Process (BP)	nitrogen compound transport	0.1279	Informative	Inherited
Biological Process (BP)	intracellular signal transduction	0.00459	Informative	Inherited
Biological Process (BP)	peptidyl-amino acid modification	1	Informative	Inherited
Biological Process (BP)	protein modification by small protein conjugation or removal	0.9472	Informative	Inherited
Biological Process (BP)	protein dephosphorylation	0	Highly Informative	Direct
Biological Process (BP)	negative regulation of phosphorylation	3.109e-12	Highly Informative	Direct
Biological Process (BP)	negative regulation of protein modification process	4.856e-11	Highly Informative	Direct
Biological Process (BP)	negative regulation of signal transduction	2.991e-10	Highly Informative	Direct
Biological Process (BP)	cell projection assembly	5.672e-06	Highly Informative	Direct
Biological Process (BP)	stress-activated protein kinase signaling cascade	1.117e-05	Highly Informative	Direct
Biological Process (BP)	cell cycle phase transition	2.759e-05	Highly Informative	Direct
Biological Process (BP)	regulation of MAP kinase activity	2.811e-05	Highly Informative	Direct
Biological Process (BP)	cellular component assembly involved in morphogenesis	5.335e-05	Highly Informative	Direct
Biological Process (BP)	mitochondrial transport	0.0004443	Highly Informative	Direct
Biological Process (BP)	MAPK cascade	0.0008537	Highly Informative	Direct
Biological Process (BP)	mitotic cell cycle	0.1611	Highly Informative	Inherited
Molecular Function (MF)	hydrolase activity	1.28e-10	Least Informative	Direct
Molecular Function (MF)	transferase activity	1	Least Informative	Inherited
Molecular Function (MF)	binding	1	Least Informative	Inherited
Molecular Function (MF)	hydrolase activity, acting on ester bonds	0	Moderately Informative	Direct
Molecular Function (MF)	heterocyclic compound binding	1	Moderately Informative	Inherited
Molecular Function (MF)	organic cyclic compound binding	1	Moderately Informative	Inherited
Molecular Function (MF)	phosphoric ester hydrolase activity	0	Informative	Direct
Molecular Function (MF)	peptidase activity	1	Informative	Inherited
Molecular Function (MF)	RNA binding	0.593	Informative	Inherited
Molecular Function (MF)	sulfurtransferase activity	0	Highly Informative	Direct
Molecular Function (MF)	phosphoprotein phosphatase activity	5.349e-06	Highly Informative	Direct
Cellular Component (CC)	intracellular organelle part	1	Least Informative	Inherited
Cellular Component (CC)	membrane	1	Least Informative	Inherited
Cellular Component (CC)	cytoplasmic part	0.5075	Least Informative	Inherited
Cellular Component (CC)	intracellular non-membrane-bounded organelle	1	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	0.02945	Least Informative	Inherited
Cellular Component (CC)	cell projection	0.0644	Moderately Informative	Inherited
Cellular Component (CC)	cytoskeleton	0.3807	Moderately Informative	Inherited
Cellular Component (CC)	vesicle	0.736	Moderately Informative	Inherited
Cellular Component (CC)	plastid	0.0001659	Informative	Direct
Cellular Component (CC)	cell projection part	0.01484	Informative	Inherited
Cellular Component (CC)	microtubule cytoskeleton	0.01625	Informative	Inherited
Cellular Component (CC)	secretory granule	0.001835	Informative	Inherited
Cellular Component (CC)	cilium part	3.727e-09	Highly Informative	Direct
Cellular Component (CC)	acrosomal vesicle	2.446e-06	Highly Informative	Direct
Cellular Component (CC)	midbody	6.253e-06	Highly Informative	Direct
Cellular Component (CC)	microtubule organizing center	8.12e-06	Highly Informative	Direct
Cellular Component (CC)	organelle subcompartment	3.967e-05	Highly Informative	Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Acting on ester bonds	0	Least Informative	Direct
Enzyme Commission (EC)	Acting on peptide bonds (peptide hydrolases)	0.4896	Least Informative	Inherited
Enzyme Commission (EC)	Phosphoric monoester hydrolases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Omega peptidases	1.076e-09	Moderately Informative	Direct
Enzyme Commission (EC)	Protein-tyrosine-phosphatase	0	Informative	Direct
Enzyme Commission (EC)	Sulfurtransferases	0	Informative	Direct
Enzyme Commission (EC)	Phosphoprotein phosphatase	2.524e-05	Informative	Direct
Enzyme Commission (EC)	tRNA sulfurtransferase	0	Highly Informative	Direct

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)

	MP term	FDR (all)	SDMP level	Annotation (direct or inherited)
Mammalian Phenotype (MP)	cellular phenotype	0.1041	Least Informative	Inherited
Mammalian Phenotype (MP)	immune system phenotype	0.2415	Least Informative	Inherited
Mammalian Phenotype (MP)	abnormal cell death	0.009802	Moderately Informative	Inherited
Mammalian Phenotype (MP)	abnormal immune serum protein physiology	0.02394	Moderately Informative	Inherited
Mammalian Phenotype (MP)	abnormal cell differentiation	0.21	Moderately Informative	Inherited
Mammalian Phenotype (MP)	digestive/alimentary phenotype	0.2595	Moderately Informative	Inherited
Mammalian Phenotype (MP)	abnormal gland morphology	0.3493	Moderately Informative	Inherited
Mammalian Phenotype (MP)	abnormal intestine morphology	0.02653	Informative	Inherited
Mammalian Phenotype (MP)	abnormal digestive system physiology	0.06136	Informative	Inherited
Mammalian Phenotype (MP)	increased apoptosis	0.175	Informative	Inherited
Mammalian Phenotype (MP)	abnormal cell proliferation	0.2933	Informative	Inherited
Mammalian Phenotype (MP)	abnormal digestive system development	0.0002784	Highly Informative	Direct
Mammalian Phenotype (MP)	abnormal intestinal mucosa morphology	0.003348	Highly Informative	Inherited
Mammalian Phenotype (MP)	abnormal tumor necrosis factor secretion	0.05266	Highly Informative	Inherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)

	WP term	FDR (all)	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	organism environmental stimulus response variant	0.3406	Least Informative	Inherited
Worm Phenotype (WP)	organism pathogen response variant	0.001217	Informative	Inherited
Worm Phenotype (WP)	pathogen susceptibility increased	4.183e-05	Highly Informative	Direct

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)

	FA term	FDR (all)	SDFA level	Annotation (direct or inherited)
Fly Anatomy (FA)	organ system	0	Least Informative	Direct
Fly Anatomy (FA)	cell	0	Least Informative	Direct
Fly Anatomy (FA)	multi-tissue structure	0	Least Informative	Direct
Fly Anatomy (FA)	organ system subdivision	0	Least Informative	Direct
Fly Anatomy (FA)	anterior-posterior subdivision of organism	1	Least Informative	Inherited
Fly Anatomy (FA)	thoracic segment	0	Moderately Informative	Direct
Fly Anatomy (FA)	adult segment	0	Moderately Informative	Direct
Fly Anatomy (FA)	adult thorax	0	Moderately Informative	Direct
Fly Anatomy (FA)	sense organ	0	Moderately Informative	Direct
Fly Anatomy (FA)	adult integumentary system	0	Moderately Informative	Direct
Fly Anatomy (FA)	cell cluster organ	0	Moderately Informative	Direct
Fly Anatomy (FA)	tagmatic subdivision of integument	0	Moderately Informative	Direct
Fly Anatomy (FA)	extended germ band embryo	0	Informative	Direct

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)

	XA term	FDR (all)	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	embryo	0.4254	Least Informative	Inherited
Xenopus ANatomical entity (XAN)	portion of tissue	0.8449	Least Informative	Inherited
Xenopus ANatomical entity (XAN)	ectoderm	0.1148	Moderately Informative	Inherited
Xenopus ANatomical entity (XAN)	neural plate	0.0007178	Informative	Direct

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)

	AP term	FDR (all)	SDAP level	Annotation (direct or inherited)
Plant structure DEvelopment stage (PDE)	4 leaf senescence stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.12 twelve leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.06 six leaves visible stage	0	Least Informative	Direct

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Hydrolases	0.06207	Least Informative	Inherited
Enzyme Commission (EC)	Phosphoric monoester hydrolases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Acting on peptide bonds (peptide hydrolases)	0.5284	Moderately Informative	Inherited
Enzyme Commission (EC)	Protein-tyrosine-phosphatase	0	Informative	Direct
Enzyme Commission (EC)	Omega peptidases	1.694e-09	Informative	Direct
Enzyme Commission (EC)	Sulfurtransferases	0	Highly Informative	Direct
Enzyme Commission (EC)	Phosphoprotein phosphatase	4.003e-06	Highly Informative	Direct

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	Cell cycle	1.12e-10	Moderately Informative	Direct
Biological process	Mitosis	0	Informative	Direct
Biological process	Thiamine biosynthesis	0	Highly Informative	Direct
Biological process	Cilium biogenesis/degradation	4.188e-13	Highly Informative	Direct
Cellular component	Cytoplasm	0	Least Informative	Direct
Cellular component	Endosome	1.337e-05	Moderately Informative	Direct
Cellular component	Cell projection	2.27e-05	Moderately Informative	Direct
Cellular component	Cilium	5.913e-10	Highly Informative	Direct
Disease	Ciliopathy	0	Informative	Direct
Domain	Redox-active center	0	Informative	Direct
Molecular function	RNA-binding	0	Moderately Informative	Direct
Molecular function	tRNA-binding	0	Informative	Direct
Post-translational modification	Transferase	0	Least Informative	Direct
Post-translational modification	Hydrolase	0.3821	Least Informative	Inherited
Post-translational modification	Protease	0.7143	Moderately Informative	Inherited
Post-translational modification	Protein phosphatase	0	Informative	Direct
Post-translational modification	Thiol protease	2.569e-07	Informative	Direct
Post-translational modification	Disulfide bond	1.354e-12	Least Informative	Direct

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)

	UP term	FDR (all)	SDUP level	Annotation (direct or inherited)
UniPathway (UP)	cofactor metabolism	0	Least Informative	Direct
UniPathway (UP)	thiamine metabolism	0	Informative	Direct

Document: UP annotation of SCOP domains

InterPro annotation

Cross references IPR001763 SSF52821 Protein matches

Abstract
Rhodanese, a sulphurtransferase involved in cyanide detoxification (see ) 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 ).

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].

InterPro database

PDBeMotif information about ligands, sequence and structure motifs

Cross references

PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 22 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.

Browse and view proteins in genomes which have different domain combinations including a Rhodanese/Cell cycle control phosphatase domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.

Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 22 hidden Markov models representing the Rhodanese/Cell cycle control phosphatase superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

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Rhodanese/Cell cycle control phosphatase superfamily