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Cryptochrome/photolyase FAD-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Cryptochrome/photolyase FAD-binding domain [ 48172]
Superfamily:   Cryptochrome/photolyase FAD-binding domain [ 48173]
Families:   Cryptochrome/photolyase FAD-binding domain [ 48174] (2)

Superfamily statistics
Genomes (1,415) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,087 7,225 6
Proteins 3,070 7,213 6

 Functional annotation
General category General
Detailed category General

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 4.092e-05 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.01852 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) localization 0.2756 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.3118 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.00288 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.003694 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.006088 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01017 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.03464 Least Informative Inherited
Biological Process (BP) response to abiotic stimulus 1.087e-08 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 5.837e-07 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0002846 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0003212 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0003358 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.0004214 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.0005831 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0006274 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0009458 Moderately Informative Direct
Biological Process (BP) cellular localization 0.007759 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.004965 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.09722 Moderately Informative Inherited
Biological Process (BP) response to light stimulus 0 Informative Direct
Biological Process (BP) nucleocytoplasmic transport 1.647e-09 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 8.657e-09 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 1.761e-08 Informative Direct
Biological Process (BP) protein localization to organelle 7.689e-08 Informative Direct
Biological Process (BP) negative regulation of cellular metabolic process 1.766e-07 Informative Direct
Biological Process (BP) cytoplasmic transport 8.384e-07 Informative Direct
Biological Process (BP) protein transport 2.616e-06 Informative Direct
Biological Process (BP) DNA metabolic process 6.65e-06 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.007277 Informative Inherited
Biological Process (BP) protein targeting to nucleus 1.348e-11 Highly Informative Direct
Biological Process (BP) nuclear import 1.642e-11 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 6.092e-11 Highly Informative Direct
Biological Process (BP) protein import 1.492e-10 Highly Informative Direct
Biological Process (BP) DNA repair 3.279e-10 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 3.682e-09 Highly Informative Direct
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 7.746e-09 Highly Informative Direct
Biological Process (BP) negative regulation of gene expression 1.258e-08 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 1.623e-08 Highly Informative Direct
Molecular Function (MF) binding 0.1265 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 3.954e-05 Moderately Informative Direct
Molecular Function (MF) heterocyclic compound binding 0.0001018 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 0.0001204 Moderately Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) cofactor binding 3.684e-08 Informative Direct
Molecular Function (MF) receptor activity 3.783e-08 Informative Direct
Molecular Function (MF) molecular transducer activity 7e-08 Informative Direct
Molecular Function (MF) nucleotide binding 1.618e-06 Informative Direct
Cellular Component (CC) intracellular organelle part 0.1233 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.03273 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.0004352 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.002048 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.03449 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 2.277e-05 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)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)stalk0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant ANatomical entity (PAN)microgametophyte0Least 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 regulation0Moderately InformativeDirect
Biological processSensory transduction0InformativeDirect
Biological processBiological rhythms0Highly InformativeDirect
Cellular componentNucleus2.84e-11Least InformativeDirect
DomainTransit peptide0.0002079Moderately InformativeDirect
Molecular functionNucleotide-binding1.837e-05Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionFAD0InformativeDirect
Molecular functionFlavoprotein0InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationLyase8.605e-14Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond2.27e-10Moderately InformativeDirect
Post-translational modificationUbl conjugation5.491e-09Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR005101 SSF48173 Protein matches
Abstract

Deoxyribodipyrimidine photolyase (DNA photolyase) is a DNA repair enzyme. It binds to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), breaks the cyclobutane ring joining the two pyrimidines of the dimer. DNA photolyase is an enzyme that requires two choromophore-cofactors for its activity: a reduced FADH2 and either 5,10-methenyltetrahydrofolate (5,10-MTFH) or an oxidized 8-hydroxy-5- deazaflavin (8-HDF) derivative (F420). The folate or deazaflavin chromophore appears to function as an antenna, while the FADH2 chromophore is thought to be responsible for electron transfer. On the basis of sequence similarities DNA photolyases can be grouped into two classes. The first class contains enzymes from Gram-negative and Gram-positive bacteria, the halophilic archaebacteria Halobacterium halobium, fungi and plants. Class 1 enzymes bind either 5,10-MTHF (E. coli, fungi, etc.) or 8-HDF (S.griseus, H.halobium).

Proteins containing this domain also include Arabidopsis cryptochromes 1 (CRY1) and 2 (CRY2), which are blue light photoreceptors that mediate blue light-induced gene expression.


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 FAD-binding 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 FAD-binding 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 ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.