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Cryptochrome/photolyase, N-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Cryptochrome/photolyase, N-terminal domain [ 52424]
Superfamily:   Cryptochrome/photolyase, N-terminal domain [ 52425]
Families:   Cryptochrome/photolyase, N-terminal domain [ 52426] (2)


Superfamily statistics
Genomes (1,786) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,503 14,996 6
Proteins 3,477 14,971 6


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) response to stimulus 0.0000000001217 Least Informative Direct
Biological Process (BP) biological regulation 0.0000001092 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0002605 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0003119 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0004014 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000646 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.000883 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.7618 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.8184 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.03039 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000000000000003734 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.00000009432 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000001278 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.000008049 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00002194 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.9602 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.1109 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1374 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.008478 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.6694 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.5453 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.8566 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.02804 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.8762 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.9994 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.08677 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.06017 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.0247 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.06571 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.02396 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 0 Informative Direct
Biological Process (BP) response to radiation 0 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0 Informative Direct
Biological Process (BP) DNA metabolic process 0.00000009132 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.0000002854 Informative Direct
Biological Process (BP) monosaccharide metabolic process 0.000009605 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00002252 Informative Direct
Biological Process (BP) protein localization to organelle 0.0003114 Informative Direct
Biological Process (BP) regulation of cell cycle 0.3418 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.01126 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.001643 Informative Inherited
Biological Process (BP) intracellular transport 0.0231 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.01965 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.3752 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.6312 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.4814 Informative Inherited
Biological Process (BP) protein transport 0.003534 Informative Inherited
Biological Process (BP) phosphorylation 0.002178 Informative Inherited
Biological Process (BP) response to oxidative stress 0.08726 Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) circadian rhythm 0 Highly Informative Direct
Biological Process (BP) hexose biosynthetic process 0.000000006593 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.0000002131 Highly Informative Direct
Biological Process (BP) single-organism nuclear import 0.0000003801 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.0000009964 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 0.000001221 Highly Informative Direct
Biological Process (BP) protein import 0.000001717 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.00001062 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.00001133 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.00001289 Highly Informative Direct
Biological Process (BP) regulation of protein modification by small protein conjugation or removal 0.00002044 Highly Informative Direct
Biological Process (BP) response to hydrogen peroxide 0.0001498 Highly Informative Direct
Biological Process (BP) photoperiodism 0.0002732 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0321 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.03333 Highly Informative Inherited
Molecular Function (MF) binding 0.4883 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.00000003742 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0000003106 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1 Moderately Informative Inherited
Molecular Function (MF) coenzyme binding 0 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0.000000002334 Informative Direct
Molecular Function (MF) signal transducer activity 0.000000004971 Informative Direct
Molecular Function (MF) DNA binding 0.01899 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.00001901 Highly Informative Direct
Cellular Component (CC) membrane 0.6538 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.0574 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0.00000007302 Moderately Informative Direct
Cellular Component (CC) cell projection 0.0003215 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.4603 Moderately Informative Inherited
Cellular Component (CC) plasma membrane region 0.0000000006521 Informative Direct
Cellular Component (CC) cilium 0.000000001079 Informative Direct
Cellular Component (CC) plasma membrane bounded cell projection part 0.000000004615 Informative Direct
Cellular Component (CC) neuron projection 0.00000003232 Informative Direct
Cellular Component (CC) photoreceptor cell cilium 0 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)Other carbon-carbon lyases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processTranscription regulation7.256e-16Moderately InformativeDirect
Biological processDNA repair0InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processSensory transduction0InformativeDirect
Cellular componentNucleus0.000000000497Least InformativeDirect
DomainTransit peptide0.000213Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionFAD0InformativeDirect
Molecular functionChromophore0InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationLyase0.00000000000001502Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond0.00000002485Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0000001292Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006050 SSF52425 Protein matches
Abstract

DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation [PubMed6325459]. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light [PubMed3000886]. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain [PubMed6325459]. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [PubMed3000886, PubMed2110564]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm [PubMed2110564].

This domain binds a light harvesting cofactor.


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-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 5 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 Cryptochrome/photolyase, N-terminal domain 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 5 hidden Markov models representing the Cryptochrome/photolyase, N-terminal domain 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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]