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Nucleotide cyclase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   Nucleotide cyclase [ 55073] (2)
Families:   Adenylyl and guanylyl cyclase catalytic domain [ 55074] (5)
  GGDEF domain [ 117984]


Superfamily statistics
Genomes (2,322) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 38,878 234,520 11
Proteins 36,901 229,317 11


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) 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 aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00000000001174 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.00005699 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0000005347 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.3351 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.06665 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) cell communication 0.0000000000001202 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) single organism signaling 0 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.0002193 Moderately Informative Direct
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.3458 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.9967 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.6555 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.9266 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.9311 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) system process 0 Informative Direct
Biological Process (BP) behavior 0.0000002317 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.00000001758 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0.0009106 Informative Direct
Biological Process (BP) intracellular signal transduction 0.000000005187 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0 Informative Direct
Biological Process (BP) cellular response to inorganic substance 0.000001071 Informative Direct
Biological Process (BP) cellular response to lipid 0.0000001304 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0 Informative Direct
Biological Process (BP) response to nitrogen compound 0.000155 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.000001372 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.4983 Informative Inherited
Biological Process (BP) regulation of locomotion 0.08765 Informative Inherited
Biological Process (BP) response to oxidative stress 0.002461 Informative Inherited
Biological Process (BP) regulation of hormone levels 0.4398 Informative Inherited
Biological Process (BP) regulation of protein localization 0.8508 Informative Inherited
Biological Process (BP) regulation of secretion 0.1532 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.7156 Informative Inherited
Biological Process (BP) regulation of peptide transport 0.6215 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.5844 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.609 Informative Inherited
Biological Process (BP) regulation of phosphorylation 1 Informative Inherited
Biological Process (BP) regulation of transferase activity 0.114 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.2952 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.6317 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.2824 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.02336 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.8886 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) locomotion 0.002897 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 0.01427 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.2081 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 1 Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.00000006083 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.0005228 Highly Informative Direct
Biological Process (BP) second-messenger-mediated signaling 0 Highly Informative Direct
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.0001977 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.0000000009097 Highly Informative Direct
Biological Process (BP) positive regulation of nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) multicellular organismal homeostasis 0.000002629 Highly Informative Direct
Biological Process (BP) response to ketone 0.00000000549 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.03445 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular component movement 0.002121 Highly Informative Inherited
Biological Process (BP) cellular response to reactive oxygen species 0.07665 Highly Informative Inherited
Biological Process (BP) cellular response to organonitrogen compound 0.0535 Highly Informative Inherited
Biological Process (BP) regulation of hormone secretion 0.02737 Highly Informative Inherited
Biological Process (BP) multi-organism cellular process 0.002196 Highly Informative Inherited
Biological Process (BP) response to carbohydrate 0.0111 Highly Informative Inherited
Biological Process (BP) activation of protein kinase activity 0.0135 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.2801 Highly Informative Inherited
Biological Process (BP) plasma membrane bounded cell projection organization 1 Highly Informative Inherited
Biological Process (BP) neuron development 0.3934 Highly Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.004921 Highly Informative Inherited
Biological Process (BP) nervous system process 0.1472 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.5199 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 1 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.03626 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.000000000004124 Informative Direct
Molecular Function (MF) tetrapyrrole binding 0.00001554 Informative Direct
Molecular Function (MF) molecular transducer activity 0.00002785 Informative Direct
Molecular Function (MF) protein dimerization activity 0.05001 Informative Inherited
Molecular Function (MF) signal transducer activity 0.1779 Informative Inherited
Molecular Function (MF) enzyme binding 0.4941 Informative Inherited
Molecular Function (MF) phosphoric diester hydrolase activity 0.000004696 Highly Informative Direct
Molecular Function (MF) heme binding 0.0000105 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.000000001832 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0009519 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) membrane 0.003736 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.0000009 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.000000001044 Moderately Informative Direct
Cellular Component (CC) cell projection 0.0000000003191 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0.00002306 Moderately Informative Direct
Cellular Component (CC) cilium 0 Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0.000007165 Highly Informative Direct
Cellular Component (CC) motile cilium 0.0003661 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.01671Least InformativeInherited
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited
Enzyme Commission (EC)Adenylate cyclase0Highly InformativeDirect
Enzyme Commission (EC)Guanylate cyclase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processSensory transduction0InformativeDirect
Biological processChemotaxis0.0000000002394InformativeDirect
Biological processOsteogenesis0.000000001103Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell projection0Moderately InformativeDirect
Cellular componentCell membrane0.0000000005027Moderately InformativeDirect
Cellular componentCilium0.00009497InformativeDirect
Cellular componentFlagellum0.0001654Highly InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding0.0001245Least InformativeDirect
Molecular functionManganese0.0000000002335Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functionHeme0.000003855InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationCalmodulin-binding0.00000005858InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001054 SSF55073 Protein matches
Abstract

Guanylate cyclases catalyse the formation of cyclic GMP (cGMP) from GTP. cGMP acts as an intracellular messenger, activating cGMP-dependent kinases and regulating cGMP-sensitive ion channels. The role of cGMP as a second messenger in vascular smooth muscle relaxation and retinal photo-transduction is well established. Guanylate cyclase is found both in the soluble and particulate fractions of eukaryotic cells. The soluble and plasma membrane-bound forms differ in structure, regulation and other properties [PubMed1349465, PubMed1356629, PubMed1680765, PubMed1982420]. Most currently known plasma membrane-bound forms are receptors for small polypeptides. The soluble forms of guanylate cyclase are cytoplasmic heterodimers having alpha and beta subunits.

In all characterised eukaryote guanylyl- and adenylyl cyclases, cyclic nucleotide synthesis is carried out by the conserved class III cyclase domain.


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 6 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 Nucleotide cyclase 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 6 hidden Markov models representing the Nucleotide cyclase 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 ]