SUPERFAMILY 1.75 HMM library and genome assignments server

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 (1,781) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,495 13,801 6
Proteins 3,469 13,790 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 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.000007165 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00004808 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0002178 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.002278 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.6254 Least Informative Inherited
Biological Process (BP) localization 0.3896 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.0212 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.0316 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.6774 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1629 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1697 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1815 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2384 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00000000000002922 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0000000000002075 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00000000004787 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0000000001192 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0000000003314 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000000008706 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000001633 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.000003073 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000004638 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.000238 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0007811 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.6873 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.3206 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.01693 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.01923 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.4467 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.006198 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.3688 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.06999 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.003838 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.002914 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.006861 Moderately Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0 Informative Direct
Biological Process (BP) response to light stimulus 0 Informative Direct
Biological Process (BP) DNA repair 0.0000000002751 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.0000000913 Informative Direct
Biological Process (BP) hexose metabolic process 0.0000009097 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.000006157 Informative Direct
Biological Process (BP) protein localization to organelle 0.00001001 Informative Direct
Biological Process (BP) regulation of cell cycle process 0.00002971 Informative Direct
Biological Process (BP) cytoplasmic transport 0.00005788 Informative Direct
Biological Process (BP) single-organism cellular localization 0.0001049 Informative Direct
Biological Process (BP) protein transport 0.0001123 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.0006494 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.004523 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.007057 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.1994 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.002388 Informative Inherited
Biological Process (BP) phosphorylation 0.007621 Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-templated 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) regulation of protein ubiquitination 0.000000005977 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 0.000000009268 Highly Informative Direct
Biological Process (BP) single-organism nuclear import 0.000000009381 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.00000001395 Highly Informative Direct
Biological Process (BP) protein import 0.00000005959 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.0000003287 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.0000007581 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.00001346 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.000193 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0.0007086 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0008305 Highly Informative Direct
Biological Process (BP) cellular response to radiation 0.005549 Highly Informative Inherited
Molecular Function (MF) binding 0.007973 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000000007673 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.00000002974 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.9696 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) cofactor binding 0.000000000002106 Informative Direct
Molecular Function (MF) nucleotide binding 0.00000000005385 Informative Direct
Molecular Function (MF) receptor activity 0.0000001352 Informative Direct
Molecular Function (MF) molecular transducer activity 0.0000002071 Informative Direct
Molecular Function (MF) DNA binding 0.0187 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.000000002302 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.001257 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0Moderately 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 regulation2.372e-16Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processSensory transduction0InformativeDirect
Cellular componentNucleus0.0000000001472Least InformativeDirect
DomainTransit peptide0.0001991Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionNucleotide-binding0.00001638Least InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationLyase0.00000000000003842Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond0.0000000002758Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000000007251Moderately 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) · 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 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]