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 (2,446) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 20,791 42,742 2
Proteins 20,477 42,534 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 process0.00000000000062220Moderately InformativeDirect
Biological Process (BP)dephosphorylation00InformativeDirect
Molecular Function (MF)hydrolase activity0.00000000088510Least InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)phosphatase activity00InformativeDirect
Molecular Function (MF)phosphoprotein phosphatase activity0.000000000095570Highly 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) response to stimulus 0.000003263 Least Informative Direct
Biological Process (BP) protein metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.000009825 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.8022 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.8955 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.7377 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 0.00003343 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.000000000000003707 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0.00000000000005193 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00000000000413 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.0000003689 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000003268 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.000004088 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.02018 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.008056 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.781 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.1426 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.7231 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.02538 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.00123 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.0117 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.007475 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8468 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.2918 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.7429 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.3466 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 protein phosphorylation 0 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 0 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.00000000000005029 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.00000000000745 Informative Direct
Biological Process (BP) positive regulation of cell death 0.0000000004537 Informative Direct
Biological Process (BP) regulation of transferase activity 0.000000001076 Informative Direct
Biological Process (BP) apoptotic process 0.000000001582 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.00000001322 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.00000001552 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.0000003856 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0000005984 Informative Direct
Biological Process (BP) negative regulation of signaling 0.000002153 Informative Direct
Biological Process (BP) regulation of locomotion 0.000002747 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.000008934 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.00001523 Informative Direct
Biological Process (BP) regulation of growth 0.00003011 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.00003297 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.0000392 Informative Direct
Biological Process (BP) intracellular signal transduction 0.0001055 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.0003512 Informative Direct
Biological Process (BP) negative regulation of transport 0.0004339 Informative Direct
Biological Process (BP) positive regulation of gene expression 0.001821 Informative Inherited
Biological Process (BP) response to lipid 0.08755 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.005586 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.001154 Informative Inherited
Biological Process (BP) regulation of MAPK cascade 0.791 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.7693 Informative Inherited
Biological Process (BP) regulation of protein localization 0.2454 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 0.03732 Informative Inherited
Biological Process (BP) cellular response to hormone stimulus 0.284 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.9448 Informative Inherited
Biological Process (BP) response to acid chemical 0.003701 Informative Inherited
Biological Process (BP) response to inorganic substance 0.3546 Informative Inherited
Biological Process (BP) cell cycle process 0.09957 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.08433 Informative Inherited
Biological Process (BP) protein dephosphorylation 0 Highly Informative Direct
Biological Process (BP) positive regulation of endopeptidase activity 0 Highly Informative Direct
Biological Process (BP) regulation of cysteine-type endopeptidase activity involved in apoptotic process 0 Highly Informative Direct
Biological Process (BP) positive regulation of cellular component biogenesis 0.000000000000001913 Highly Informative Direct
Biological Process (BP) negative regulation of transferase activity 0.000000000000001913 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.000000000000003707 Highly Informative Direct
Biological Process (BP) positive regulation of behavior 0.00000000000003735 Highly Informative Direct
Biological Process (BP) negative regulation of protein phosphorylation 0.00000000000005349 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.0000000000000567 Highly Informative Direct
Biological Process (BP) regulation of chemotaxis 0.00000000000362 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0.0000000000304 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 0.00000000003588 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.0000000002798 Highly Informative Direct
Biological Process (BP) regulation of protein targeting 0.000000001762 Highly Informative Direct
Biological Process (BP) regulation of protein localization to nucleus 0.000000003202 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 0.000000004083 Highly Informative Direct
Biological Process (BP) response to drug 0.0000001092 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular signal transduction 0.0000001189 Highly Informative Direct
Biological Process (BP) response to cold 0.000004156 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.000004344 Highly Informative Direct
Biological Process (BP) response to water deprivation 0.000004758 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 0.000006928 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-templated 0.000008811 Highly Informative Direct
Biological Process (BP) regulation of peptide transport 0.00001031 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 0.00003237 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0001781 Highly Informative Direct
Biological Process (BP) response to alcohol 0.001454 Highly Informative Inherited
Biological Process (BP) regulation of protein serine/threonine kinase activity 1 Highly Informative Inherited
Biological Process (BP) response to salt stress 0.3376 Highly Informative Inherited
Biological Process (BP) cellular response to acid chemical 0.126 Highly Informative Inherited
Biological Process (BP) hormone-mediated signaling pathway 0.01118 Highly Informative Inherited
Biological Process (BP) mitotic cell cycle phase transition 0.008168 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 0.0002556 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.03358 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 cyclase0.0000000001315Highly 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)morphology0.2926Moderately InformativeInherited
Yeast Phenotype (YP)subcellular morphology0.05028InformativeInherited

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)fertile0Moderately 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)Phosphorus-oxygen lyases1InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine phosphatase0Highly InformativeDirect
Enzyme Commission (EC)Adenylate cyclase0.0000000001212Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0.00004044Moderately InformativeDirect
Coding sequence diversityAlternative splicing0.00004065Least InformativeDirect
DomainTransit peptide0.0002784Moderately InformativeDirect
DomainLeucine-rich repeat0.0000000002831InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationProtein phosphatase0InformativeDirect
Post-translational modificationMyristate0.00000009296InformativeDirect

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 ]