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DNase I-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   DNase I-like [ 56218]
Superfamily:   DNase I-like [ 56219] (3)
Families:   DNase I-like [ 56220] (6)
  Inositol polyphosphate 5-phosphatase (IPP5) [ 64422] (2)
  Sphingomyelin phosphodiesterase-like [ 143902]


Superfamily statistics
Genomes (2,882) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 26,995 110,021 17
Proteins 26,636 109,211 17


Functional annotation
General category Information
Detailed category DNA replication/repair

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)cellular nitrogen compound metabolic process0.000060860.0007024Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.00088131Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.00020640.04383Least InformativeInherited
Biological Process (BP)primary metabolic process0.01810.00001067Least InformativeInherited
Biological Process (BP)response to stimulus0.20740.009503Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.00006610.03733Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.00006840.02833Least InformativeInherited
Biological Process (BP)cellular response to stress0.000011970.000006473Moderately InformativeDirect
Biological Process (BP)DNA metabolic process0.0000000000000091160.0000000000002226InformativeDirect
Molecular Function (MF)hydrolase activity0.00000001920Least InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds7.1e-160Moderately InformativeDirect
Molecular Function (MF)nuclease activity0.000000018850.008525InformativeInherited
Molecular Function (MF)deoxyribonuclease activity0.000000084520.0002375Highly 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) cellular nitrogen compound metabolic process 0.0007024 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00001067 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0000000001101 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.8557 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 0.8212 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.4236 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.04383 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.02833 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.03733 Least Informative Inherited
Biological Process (BP) response to stimulus 0.009503 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.003019 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.000006473 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000000231 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.000007027 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00004544 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.9915 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.9989 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.05167 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.723 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.08433 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.2766 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.2976 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.005269 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.09299 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.1475 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.8646 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.1806 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.009327 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.6551 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.2292 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02654 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.7568 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.05236 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.5982 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2907 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.1733 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.106 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.2843 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.4166 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.01701 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.009933 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.0000000000002226 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.0000009524 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00000000009794 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00000000000007302 Informative Direct
Biological Process (BP) phospholipid metabolic process 0 Informative Direct
Biological Process (BP) glycerolipid metabolic process 0 Informative Direct
Biological Process (BP) alcohol metabolic process 0 Informative Direct
Biological Process (BP) single-organism cellular localization 0.000000000007473 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.0000000004574 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0000001627 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.0000003968 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0000005854 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.000002279 Informative Direct
Biological Process (BP) organelle localization 0.000006351 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.000007204 Informative Direct
Biological Process (BP) ammonium ion metabolic process 0.00004325 Informative Direct
Biological Process (BP) interspecies interaction between organisms 0.0002268 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.0004655 Informative Direct
Biological Process (BP) regulation of system process 0.0005135 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0005651 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0007465 Informative Direct
Biological Process (BP) positive regulation of transport 0.0007542 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0.0009926 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.3095 Informative Inherited
Biological Process (BP) regulation of protein localization 0.1311 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.007282 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.02252 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.02446 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.007747 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.002534 Informative Inherited
Biological Process (BP) regulation of peptide transport 0.05098 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.01997 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.8997 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.04867 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.002078 Informative Inherited
Biological Process (BP) negative regulation of transport 0.003221 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.07583 Informative Inherited
Biological Process (BP) regulation of transferase activity 0.01038 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.9327 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.0043 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.0231 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.03951 Informative Inherited
Biological Process (BP) cell development 0.6404 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.8053 Informative Inherited
Biological Process (BP) single organism reproductive process 0.8985 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.9912 Informative Inherited
Biological Process (BP) system process 0.003628 Informative Inherited
Biological Process (BP) intracellular transport 0.00475 Informative Inherited
Biological Process (BP) lipid catabolic process 1 Informative Inherited
Biological Process (BP) regulation of ion transport 0.001583 Informative Inherited
Biological Process (BP) response to radiation 0.0197 Informative Inherited
Biological Process (BP) behavior 0.1527 Informative Inherited
Biological Process (BP) single-organism membrane organization 0.00758 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.02157 Informative Inherited
Biological Process (BP) membrane lipid metabolic process 0.04422 Informative Inherited
Biological Process (BP) lipid modification 0 Highly Informative Direct
Biological Process (BP) polyol metabolic process 0 Highly Informative Direct
Biological Process (BP) alcohol catabolic process 0 Highly Informative Direct
Biological Process (BP) phosphatidylinositol metabolic process 0 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0 Highly Informative Direct
Biological Process (BP) cell projection assembly 0.00000000000009057 Highly Informative Direct
Biological Process (BP) regulation of generation of precursor metabolites and energy 0.00000000001346 Highly Informative Direct
Biological Process (BP) regulation of RNA stability 0.00000000006878 Highly Informative Direct
Biological Process (BP) ceramide metabolic process 0.0000000001626 Highly Informative Direct
Biological Process (BP) establishment of organelle localization 0.0000000001861 Highly Informative Direct
Biological Process (BP) regulation of viral process 0.000000000796 Highly Informative Direct
Biological Process (BP) interaction with symbiont 0.0000000008665 Highly Informative Direct
Biological Process (BP) response to organophosphorus 0.000000001373 Highly Informative Direct
Biological Process (BP) regulation of carbohydrate biosynthetic process 0.000000002925 Highly Informative Direct
Biological Process (BP) positive regulation of homeostatic process 0.000000007704 Highly Informative Direct
Biological Process (BP) negative regulation of carbohydrate metabolic process 0.00000001055 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.0000000125 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.00000001866 Highly Informative Direct
Biological Process (BP) negative regulation of supramolecular fiber organization 0.00000002908 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 0.00000004163 Highly Informative Direct
Biological Process (BP) negative regulation of transferase activity 0.00000006973 Highly Informative Direct
Biological Process (BP) regulation of calcium ion transport 0.00000009215 Highly Informative Direct
Biological Process (BP) negative regulation of cytoskeleton organization 0.0000008293 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 0.000001674 Highly Informative Direct
Biological Process (BP) pigmentation 0.000001862 Highly Informative Direct
Biological Process (BP) negative regulation of multi-organism process 0.00000274 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 0.000002938 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.000003353 Highly Informative Direct
Biological Process (BP) negative regulation of establishment of protein localization 0.000003631 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.000004158 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism involved in symbiotic interaction 0.000005881 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0.000007494 Highly Informative Direct
Biological Process (BP) protein localization to membrane 0.000007856 Highly Informative Direct
Biological Process (BP) negative regulation of phosphate metabolic process 0.000008208 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.000008755 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular signal transduction 0.00001993 Highly Informative Direct
Biological Process (BP) demethylation 0.00002864 Highly Informative Direct
Biological Process (BP) endomembrane system organization 0.00003232 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.0002812 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.0002919 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0.0005649 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.0006268 Highly Informative Direct
Biological Process (BP) response to growth factor 0.0008702 Highly Informative Direct
Biological Process (BP) germ cell development 0.3504 Highly Informative Inherited
Biological Process (BP) camera-type eye development 0.00105 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.1025 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.002659 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 0.01243 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.1049 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.3973 Moderately Informative Inherited
Molecular Function (MF) phosphatase activity 0.8003 Informative Inherited
Molecular Function (MF) signal transducer activity 0.773 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.6926 Informative Inherited
Molecular Function (MF) nuclease activity 0.008525 Informative Inherited
Molecular Function (MF) DNA binding 0.06316 Informative Inherited
Molecular Function (MF) deoxyribonuclease activity 0.0002375 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 0 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.00000005158 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0.000005988 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0.2129 Highly Informative Inherited
Molecular Function (MF) chromatin binding 0.0844 Highly Informative Inherited
Molecular Function (MF) transmembrane signaling receptor activity 0.1584 Highly Informative Inherited
Molecular Function (MF) lipase activity 1 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0003364 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.2235 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.1156 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.00000000002702 Moderately Informative Direct
Cellular Component (CC) cell projection 0.001418 Moderately Informative Inherited
Cellular Component (CC) nuclear part 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) plasma membrane bounded cell projection part 0.00001695 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0002323 Informative Direct
Cellular Component (CC) plasma membrane region 0.0002498 Informative Direct
Cellular Component (CC) Golgi apparatus 0.007483 Informative Inherited
Cellular Component (CC) cis-Golgi network 0 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0 Highly Informative Direct
Cellular Component (CC) CCR4-NOT complex 0 Highly Informative Direct
Cellular Component (CC) ruffle 0.00000000001831 Highly Informative Direct
Cellular Component (CC) Golgi subcompartment 0.000003289 Highly Informative Direct
Cellular Component (CC) nuclear body 0.00002785 Highly Informative Direct

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)Lyases0.2093Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.6315Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0.000005811Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.004367Moderately InformativeInherited
Enzyme Commission (EC)Other carbon-oxygen lyases0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0.00000000038InformativeDirect
Enzyme Commission (EC)DNA-(apurinic or apyrimidinic site) lyase0Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0Highly InformativeDirect
Enzyme Commission (EC)Phosphatidylinositol-3,4,5-trisphosphate 5-phospha4.713e-16Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonuclease III0.000000000000008279Highly InformativeDirect
Enzyme Commission (EC)Endodeoxyribonucleases producing 5'-phosphomonoest0.00007384Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0.000000000000008233Moderately InformativeDirect
Biological processApoptosis0.00000000000004511Moderately InformativeDirect
Biological processDNA damage0.000000000005187Moderately InformativeDirect
Biological processLipid metabolism0.0000007408Moderately InformativeDirect
Biological processImmunity0.000001497Moderately InformativeDirect
Biological processDNA repair0.00000000000231InformativeDirect
Biological processEndocytosis0.000000001135InformativeDirect
Biological processmRNA processing0.000000009111InformativeDirect
Biological processCytolysis0.0000001177InformativeDirect
Biological processTranslation regulation0.000005092InformativeDirect
Biological processDNA recombination0.00003071InformativeDirect
Biological processSphingolipid metabolism0Highly InformativeDirect
Biological processRNA-mediated gene silencing0.0000000000421Highly InformativeDirect
Biological processHemolysis0.000000009894Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm0.1765Least InformativeInherited
Cellular componentEndoplasmic reticulum0.00000000004197Moderately InformativeDirect
Cellular componentCell projection0.000000001113Moderately InformativeDirect
Cellular componentCytoskeleton0.0000002774Moderately InformativeDirect
Cellular componentGolgi apparatus0.00004901Moderately InformativeDirect
Cellular componentSecreted0.0008186Moderately InformativeDirect
DomainRepeat0.00008696Least InformativeDirect
DomainLeucine-rich repeat0InformativeDirect
DomainSH3-binding6.227e-16InformativeDirect
DomainSH2 domain0.0000000002231InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0.00000000009868Least InformativeDirect
Molecular functionCalcium0.00000007845Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationActivator0.00000000001236Moderately InformativeDirect
Post-translational modificationRepressor0.00000001266Moderately InformativeDirect
Post-translational modificationRNA-binding0.00000002091Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.2793Moderately InformativeInherited
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationActin-binding0.0000000000000235InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0.000000000001784Highly InformativeDirect
Post-translational modificationS-nitrosylation0.0000001969InformativeDirect
Post-translational modificationPrenylation0.0004384InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR005135 SSF56219 Protein matches
Abstract

This domain is found in a large number of proteins including magnesium dependent endonucleases and phosphatases involved in intracellular signalling [PubMed10838565]. Proteins this domain is found in include: AP endonuclease proteins , DNase I proteins , Synaptojanin an inositol-1,4,5-trisphosphate phosphatase and Sphingomyelinase .


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 11 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 DNase I-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 11 hidden Markov models representing the DNase I-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 ]