SUPERFAMILY 1.75 HMM library and genome assignments server


PP2C-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   PP2C-like [ 81607]
Superfamily:   PP2C-like [ 81606]
Families:   PP2C-like [ 81605] (2)


Superfamily statistics
Genomes (2,402) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 18,057 22,577 2
Proteins 17,869 22,448 2


Functional annotation
General category Regulation
Detailed category Kinases/phosphatases

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)phosphate-containing compound metabolic process1.393e-130Moderately InformativeDirect
Biological Process (BP)dephosphorylation00InformativeDirect
Molecular Function (MF)hydrolase activity6.21e-100Least InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)phosphatase activity00InformativeDirect
Molecular Function (MF)phosphoprotein phosphatase activity8.876e-110Highly InformativeDirect

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 0 Least Informative Direct
Biological Process (BP) response to stimulus 4.773e-06 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 5.226e-07 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.8054 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.7507 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) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) signal transduction 7.162e-06 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 3.746e-15 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1.219e-12 Moderately Informative Direct
Biological Process (BP) regulation of programmed cell death 1.189e-08 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 8.515e-07 Moderately Informative Direct
Biological Process (BP) regulation of localization 8.915e-07 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 3.545e-06 Moderately Informative Direct
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.659 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.04787 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.01496 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.408 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.001047 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.03528 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.001125 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.09039 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.02168 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.1104 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) dephosphorylation 0 Informative Direct
Biological Process (BP) regulation of kinase activity 0 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 2.195e-10 Informative Direct
Biological Process (BP) regulation of peptidase activity 2.311e-10 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 2.395e-09 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 4.986e-09 Informative Direct
Biological Process (BP) cell death 1.175e-08 Informative Direct
Biological Process (BP) regulation of cellular component movement 4.511e-07 Informative Direct
Biological Process (BP) negative regulation of signaling 1.71e-06 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 1.748e-06 Informative Direct
Biological Process (BP) regulation of locomotion 2.027e-06 Informative Direct
Biological Process (BP) negative regulation of cell communication 4.687e-06 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 1.508e-05 Informative Direct
Biological Process (BP) regulation of intracellular protein kinase cascade 2.112e-05 Informative Direct
Biological Process (BP) regulation of growth 2.859e-05 Informative Direct
Biological Process (BP) intracellular signal transduction 4.591e-05 Informative Direct
Biological Process (BP) positive regulation of gene expression 0.0002837 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.0003279 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.0004867 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0005044 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.0006258 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0009482 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.9258 Informative Inherited
Biological Process (BP) response to lipid 0.02087 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.06978 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.4917 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.005366 Informative Inherited
Biological Process (BP) response to inorganic substance 0.2499 Informative Inherited
Biological Process (BP) cell cycle process 0.136 Informative Inherited
Biological Process (BP) protein dephosphorylation 0 Highly Informative Direct
Biological Process (BP) positive regulation of peptidase activity 0 Highly Informative Direct
Biological Process (BP) regulation of cysteine-type endopeptidase activity 0 Highly Informative Direct
Biological Process (BP) positive regulation of growth 1.931e-15 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 1.931e-15 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 5.078e-14 Highly Informative Direct
Biological Process (BP) negative regulation of phosphorylation 6.85e-14 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 4.852e-13 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 7.973e-11 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 1.398e-10 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 2.875e-09 Highly Informative Direct
Biological Process (BP) regulation of protein localization to nucleus 5.675e-09 Highly Informative Direct
Biological Process (BP) regulation of behavior 1.914e-08 Highly Informative Direct
Biological Process (BP) response to drug 3.523e-08 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 2.606e-06 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 2.993e-06 Highly Informative Direct
Biological Process (BP) response to cold 6.886e-06 Highly Informative Direct
Biological Process (BP) response to water deprivation 7.711e-06 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 1.123e-05 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 3.476e-05 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 9.144e-05 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.0001371 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0003238 Highly Informative Direct
Biological Process (BP) cellular response to alcohol 0.0007716 Highly Informative Direct
Biological Process (BP) response to osmotic stress 0.003064 Highly Informative Inherited
Biological Process (BP) hormone-mediated signaling pathway 0.01257 Highly Informative Inherited
Biological Process (BP) mitotic cell cycle phase transition 0.01487 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) phosphatase activity 0 Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 1.085e-05 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.3183 Least Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoprotein phosphatase0InformativeDirect
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited
Enzyme Commission (EC)Adenylate cyclase1.315e-10Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)morphology0.277Moderately InformativeInherited
Yeast Phenotype (YP)subcellular morphology0.04096InformativeInherited

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Least InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)sporangium0.0001919Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0.04927Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll0.2479Least InformativeInherited

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine phosphatase0Highly InformativeDirect
Enzyme Commission (EC)Adenylate cyclase1.087e-10Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis3.903e-05Moderately InformativeDirect
Coding sequence diversityAlternative splicing0.0001641Least InformativeDirect
DomainTransit peptide0.0002441Moderately InformativeDirect
DomainLeucine-rich repeat2.834e-10InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationProtein phosphatase0InformativeDirect
Post-translational modificationMyristate9.062e-08InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001932 SSF81606 Protein matches
Abstract

This domain is found in protein phosphatase 2C, as well as other proteins eg. pyruvate dehydrogenase (lipoamide)]-phosphatase and adenylate cyclase .

Protein phosphatase 2C (PP2C) is one of the four major classes of mammalian serine/threonine specific protein phosphatases . PP2C [PubMed1312947] is a monomeric enzyme of about 42 Kd which shows broad substrate specificity and is dependent on divalent cations (mainly manganese and magnesium) for its activity. Its exact physiological role is still unclear. Three isozymes are currently known in mammals: PP2C-alpha, -beta and -gamma. In yeast, there are at least four PP2C homologs: phosphatase PTC1 [PubMed8395005], which has weak tyrosine phosphatase activity in addition to its activity on serines, phosphatases PTC2 and PTC3, and hypothetical protein YBR125c. Isozymes of PP2C are also known from Arabidopsis thaliana (ABI1, PPH1), Caenorhabditis elegans (FEM-2, F42G9.1, T23F11.1), Leishmania chagasi and Paramecium tetraurelia. In A. thaliana, the kinase associated protein phosphatase (KAPP) [PubMed7973632] is an enzyme that dephosphorylates the Ser/Thr receptor-like kinase RLK5 and which contains a C-terminal PP2C domain.

PP2C does not seem to be evolutionary related to the main family of serine/ threonine phosphatases: PP1, PP2A and PP2B. However, it is significantly similar to the catalytic subunit of pyruvate dehydrogenase phosphatase (PDPC) [PubMed8396421], which catalyzes dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex. PDPC is a mitochondrial enzyme and, like PP2C, is magnesium-dependent.


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) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 2 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 PP2C-like 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 2 hidden Markov models representing the PP2C-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


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