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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 (1,780) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,475 13,801 6
Proteins 3,449 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 0.000006161 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00005954 Least Informative Direct
Biological Process (BP) biosynthetic process 0.6441 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.02945 Least Informative Inherited
Biological Process (BP) localization 0.3667 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.001545 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.6724 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.003648 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1613 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1674 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1799 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2388 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.000000000000003755 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0000000000002009 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00000000004422 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000000000111 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000000000277 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000000003193 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000001462 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.000002971 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000003196 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.0002261 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0008257 Moderately Informative Direct
Biological Process (BP) cellular localization 0.1944 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.3633 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.021 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.3187 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.5535 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.003768 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.4477 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.00287 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.005092 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.006276 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 0.00000009237 Informative Direct
Biological Process (BP) hexose metabolic process 0.000002079 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.000006132 Informative Direct
Biological Process (BP) protein localization to organelle 0.000009411 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0000272 Informative Direct
Biological Process (BP) cytoplasmic transport 0.00004428 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.00007981 Informative Direct
Biological Process (BP) protein transport 0.0001098 Informative Direct
Biological Process (BP) DNA metabolic process 0.0001842 Informative Direct
Biological Process (BP) negative regulation of signaling 0.001812 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.00343 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.00509 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.1484 Informative Inherited
Biological Process (BP) phosphorylation 0.004627 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 0.000000005143 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 0.00000000927 Highly Informative Direct
Biological Process (BP) nuclear import 0.00000001073 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 0.00000001394 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 0.00000003525 Highly Informative Direct
Biological Process (BP) protein import 0.00000005971 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.0000007556 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.0000007781 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.00001263 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.0001245 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0007687 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0.0009798 Highly Informative Direct
Biological Process (BP) cellular response to radiation 0.004024 Highly Informative Inherited
Molecular Function (MF) binding 0.007448 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000000007598 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.9538 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) cofactor binding 0.000000000002246 Informative Direct
Molecular Function (MF) nucleotide binding 0.00000000005363 Informative Direct
Molecular Function (MF) receptor activity 0.0000001736 Informative Direct
Molecular Function (MF) molecular transducer activity 0.0000002637 Informative Direct
Molecular Function (MF) DNA binding 0.03423 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.00000000195 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000588 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)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon 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)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence 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 ]