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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 (1,788) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,942 15,483 6
Proteins 3,904 15,466 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 0.00000000176 Least Informative Direct
Biological Process (BP) biological regulation 0.000001443 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0001378 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0001684 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0003272 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0003527 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0005015 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.02983 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.879 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000000000000007367 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0000000000000109 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.00000001245 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000001858 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00003381 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00005055 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.8544 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.02983 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.01092 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.06593 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.03194 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.379 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.8272 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.9519 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.9794 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.01194 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.0103 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.121 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.07397 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.06038 Moderately Informative Inherited
Biological Process (BP) response to radiation 0 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 0 Informative Direct
Biological Process (BP) DNA metabolic process 0.00000002739 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.0000002256 Informative Direct
Biological Process (BP) monosaccharide metabolic process 0.00001334 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00002903 Informative Direct
Biological Process (BP) protein localization to organelle 0.00005221 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.0001155 Informative Direct
Biological Process (BP) intracellular protein transport 0.0002084 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.4508 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.3335 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.01335 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.01204 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.3474 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.9851 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.6346 Informative Inherited
Biological Process (BP) phosphorylation 0.00288 Informative Inherited
Biological Process (BP) circadian rhythm 0 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-templated 0 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 0.00000001714 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.00000003182 Highly Informative Direct
Biological Process (BP) protein import 0.0000001136 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.0000003209 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.000001112 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.000009868 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.00001469 Highly Informative Direct
Biological Process (BP) regulation of protein modification by small protein conjugation or removal 0.00002253 Highly Informative Direct
Biological Process (BP) photoperiodism 0.0002251 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.03544 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.02926 Highly Informative Inherited
Molecular Function (MF) binding 0.3252 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000000001115 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000000012 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) coenzyme binding 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0.0000000004031 Informative Direct
Molecular Function (MF) signal transducer activity 0.0000000009267 Informative Direct
Molecular Function (MF) DNA binding 0.01711 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.00001906 Highly Informative Direct
Cellular Component (CC) membrane 0.9479 Least Informative Inherited
Cellular Component (CC) macromolecular complex 0.9152 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0.000006907 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.6306 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.1207 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.001758 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.4305 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.4379 Moderately Informative Inherited
Cellular Component (CC) cilium 0.00000005346 Informative Direct
Cellular Component (CC) plasma membrane region 0.0000001278 Informative Direct
Cellular Component (CC) plasma membrane bounded cell projection part 0.0000005596 Informative Direct
Cellular Component (CC) neuron projection 0.000002177 Informative Direct
Cellular Component (CC) nuclear envelope 0.00004763 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

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible 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)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 regulation2.443e-16Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processSensory transduction0InformativeDirect
Cellular componentNucleus0.0000000002145Least InformativeDirect
DomainTransit peptide0.0002899Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationLyase0.000000000000003476Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond0.00000003926Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0000002089Moderately 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) · Xenopus Anatomy (XA) · 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]