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 (1,779) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,471 13,801 6
Proteins 3,445 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 4.643e-06 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 6.489e-05 Least Informative Direct
Biological Process (BP) biosynthetic process 0.6354 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.02737 Least Informative Inherited
Biological Process (BP) localization 0.3514 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.001489 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.6786 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.003728 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1621 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1671 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1811 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2374 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 1.705e-13 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 1.163e-10 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 2.117e-10 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 2.336e-10 Moderately Informative Direct
Biological Process (BP) homeostatic process 2.531e-08 Moderately Informative Direct
Biological Process (BP) cellular response to stress 1.293e-06 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 2.438e-06 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 2.641e-06 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.0001964 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0007711 Moderately Informative Direct
Biological Process (BP) cellular localization 0.1923 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.3563 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.3132 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.5485 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.003568 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.462 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.0027 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.004646 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.006295 Moderately Informative Inherited
Biological Process (BP) negative regulation of gene expression 0 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0 Informative Direct
Biological Process (BP) response to light stimulus 0 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 8.136e-08 Informative Direct
Biological Process (BP) hexose metabolic process 1.951e-06 Informative Direct
Biological Process (BP) response to organonitrogen compound 5.533e-06 Informative Direct
Biological Process (BP) protein localization to organelle 8.846e-06 Informative Direct
Biological Process (BP) response to hormone stimulus 2.451e-05 Informative Direct
Biological Process (BP) cytoplasmic transport 3.985e-05 Informative Direct
Biological Process (BP) response to DNA damage stimulus 8.942e-05 Informative Direct
Biological Process (BP) protein transport 0.000101 Informative Direct
Biological Process (BP) DNA metabolic process 0.0001831 Informative Direct
Biological Process (BP) negative regulation of signaling 0.001735 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.003319 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.004908 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.16 Informative Inherited
Biological Process (BP) phosphorylation 0.005003 Informative Inherited
Biological Process (BP) circadian rhythm 0 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 0 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 4.401e-09 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 8.556e-09 Highly Informative Direct
Biological Process (BP) nuclear import 9.916e-09 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 1.21e-08 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 3.189e-08 Highly Informative Direct
Biological Process (BP) protein import 5.432e-08 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 6.993e-07 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 7.151e-07 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 1.064e-05 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.0001253 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0007057 Highly Informative Direct
Biological Process (BP) cellular response to radiation 0.003929 Highly Informative Inherited
Biological Process (BP) protein phosphorylation 0.001033 Highly Informative Inherited
Molecular Function (MF) binding 0.006106 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 5.991e-09 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.9575 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) cofactor binding 1.575e-12 Informative Direct
Molecular Function (MF) nucleotide binding 4.536e-11 Informative Direct
Molecular Function (MF) receptor activity 1.634e-07 Informative Direct
Molecular Function (MF) molecular transducer activity 2.466e-07 Informative Direct
Molecular Function (MF) DNA binding 0.03351 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 1.514e-09 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0005322 Least 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

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 regulation2.37e-16Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processSensory transduction0InformativeDirect
Cellular componentNucleus1.429e-10Least InformativeDirect
DomainTransit peptide0.0001968Moderately InformativeDirect
Molecular functionNucleotide-binding1.731e-05Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationLyase3.559e-14Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond2.57e-10Moderately InformativeDirect
Post-translational modificationUbl conjugation6.837e-09Moderately 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 ]