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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 (2,452) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 20,883 77,657 2
Proteins 20,564 76,909 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)macromolecule metabolic process0.19160.00000000000001763Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.39460Least InformativeInherited
Biological Process (BP)primary metabolic process10.2777Least InformativeInherited
Biological Process (BP)cellular protein modification process0.0017670Moderately InformativeInherited
Biological Process (BP)protein dephosphorylation0.00010110Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.000000055320Least InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds0.0000000000000053890Moderately InformativeDirect
Molecular Function (MF)phosphatase activity00InformativeDirect
Molecular Function (MF)phosphoprotein phosphatase activity00Highly 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) macromolecule metabolic process 0.00000000000001763 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biological regulation 0.00001045 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.2777 Least Informative Inherited
Biological Process (BP) response to stimulus 0.0662 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000001078 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.000000000001421 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00000000001285 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.000000001008 Moderately Informative Direct
Biological Process (BP) single organism signaling 0.0000695 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) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) cell communication 0.02367 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.256 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.003697 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.1693 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.01565 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.7105 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.01113 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.1479 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.007831 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.4516 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.8614 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.09142 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.003697 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorylation 0 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.00000000000002769 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.000000002647 Informative Direct
Biological Process (BP) regulation of transferase activity 0.00000001113 Informative Direct
Biological Process (BP) cell death 0.00000001824 Informative Direct
Biological Process (BP) negative regulation of molecular function 0.00000003756 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0000002259 Informative Direct
Biological Process (BP) regulation of growth 0.0000004112 Informative Direct
Biological Process (BP) regulation of protein modification process 0.0000006417 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0000006447 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.0000008569 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.000001804 Informative Direct
Biological Process (BP) intracellular signal transduction 0.000002142 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.00001132 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.00003754 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.00004022 Informative Direct
Biological Process (BP) regulation of locomotion 0.00008568 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.0001419 Informative Direct
Biological Process (BP) regulation of proteolysis 0.0005647 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.0006679 Informative Direct
Biological Process (BP) regulation of peptide transport 0.0009234 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.01471 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.05524 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.001145 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.5559 Informative Inherited
Biological Process (BP) regulation of protein localization 0.6029 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.04941 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.7781 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 0.06678 Informative Inherited
Biological Process (BP) negative regulation of transport 0.003031 Informative Inherited
Biological Process (BP) response to acid chemical 0.001591 Informative Inherited
Biological Process (BP) regulation of immune response 1 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 1 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.7797 Informative Inherited
Biological Process (BP) protein dephosphorylation 0 Highly Informative Direct
Biological Process (BP) regulation of cysteine-type endopeptidase activity 0 Highly Informative Direct
Biological Process (BP) negative regulation of transferase activity 0 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell migration 0.000000000000001925 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.000000000000003734 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.0000000000008491 Highly Informative Direct
Biological Process (BP) positive regulation of cellular component biogenesis 0.00000000000264 Highly Informative Direct
Biological Process (BP) negative regulation of phosphate metabolic process 0.000000000005963 Highly Informative Direct
Biological Process (BP) positive regulation of cell adhesion 0.000000000007873 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.00000000001314 Highly Informative Direct
Biological Process (BP) positive regulation of proteolysis 0.00000000003992 Highly Informative Direct
Biological Process (BP) apoptotic process 0.00000000005221 Highly Informative Direct
Biological Process (BP) response to drug 0.00000000008696 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular signal transduction 0.000000003605 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0.00000003194 Highly Informative Direct
Biological Process (BP) regulation of protein localization to nucleus 0.00000009998 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 0.0000001702 Highly Informative Direct
Biological Process (BP) response to water deprivation 0.0000005024 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.0000005676 Highly Informative Direct
Biological Process (BP) regulation of protein import 0.000004599 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic process 0.00002441 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.00002655 Highly Informative Direct
Biological Process (BP) negative regulation of establishment of protein localization 0.00003863 Highly Informative Direct
Biological Process (BP) protein lipidation 0.00008183 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 0.00008948 Highly Informative Direct
Biological Process (BP) response to alcohol 0.000132 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0002299 Highly Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.0006061 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.002407 Highly Informative Inherited
Biological Process (BP) immune response-activating signal transduction 0.002472 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) metal ion binding 0.1127 Moderately Informative Inherited
Molecular Function (MF) phosphatase activity 0 Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 0 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.00001503 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.02659 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.02853 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0.00004798Moderately InformativeDirect
Biological processAbscisic acid signaling pathway0.000000006415Highly InformativeDirect
Coding sequence diversityAlternative splicing0.000004492Least InformativeDirect
DomainTransit peptide0.0002768Moderately InformativeDirect
DomainLeucine-rich repeat0.0000000004759InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationProtein phosphatase0InformativeDirect
Post-translational modificationPhosphoprotein0.00001119Least InformativeDirect
Post-translational modificationMyristate0.0000000000004932InformativeDirect

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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]