2J08 - JenaLib

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:117 , HOH A:2045	BINDING SITE FOR RESIDUE CL A 901
2	AC2	SOFTWARE	PRO A:148 , HOH A:2009	BINDING SITE FOR RESIDUE CL A 902
3	AC3	SOFTWARE	VAL A:135 , TYR A:136 , THR A:137 , ARG A:167 , ASP A:360 , HOH A:2107 , HOH A:2108	BINDING SITE FOR RESIDUE PO4 A1423
4	AC4	SOFTWARE	THR A:42 , ARG A:46 , GLU A:77 , ARG A:336 , HIS A:337	BINDING SITE FOR RESIDUE PO4 A1424
5	AC5	SOFTWARE	TYR A:197 , SER A:210 , ARG A:211 , LEU A:212 , SER A:213 , PHE A:216 , TRP A:241 , GLU A:244 , LEU A:245 , TRP A:247 , ARG A:248 , PHE A:307 , ASN A:310 , ARG A:313 , ALA A:317 , LEU A:339 , ASP A:341 , GLY A:342 , ASP A:343 , VAL A:346 , ASN A:347 , GLN A:349 , GLY A:350 , HOH A:2089 , HOH A:2096 , HOH A:2101 , HOH A:2102 , HOH A:2103	BINDING SITE FOR RESIDUE FAD A1421
6	AC6	SOFTWARE	ARG A:9 , GLY A:10 , VAL A:34 , LEU A:35 , ASP A:36 , ASN A:39 , LEU A:40 , PHE A:50 , SER A:96 , ARG A:104 , LEU A:218 , GLY A:342 , HOH A:2104 , HOH A:2105 , HOH A:2106	BINDING SITE FOR RESIDUE IRF A1422

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHR_CRY_ALPHA_BETA	PS51645	Photolyase/cryptochrome alpha/beta domain profile.	PHR_THET8	2-124	1	A:2-124
2	DNA_PHOTOLYASES_1_1	PS00394	DNA photolyases class 1 signature 1.	PHR_THET8	290-302	1	A:290-302
3	DNA_PHOTOLYASES_1_2	PS00691	DNA photolyases class 1 signature 2.	PHR_THET8	310-329	1	A:310-329

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHR_CRY_ALPHA_BETA	PS51645	Photolyase/cryptochrome alpha/beta domain profile.	PHR_THET8	2-124	1	A:2-124
2	DNA_PHOTOLYASES_1_1	PS00394	DNA photolyases class 1 signature 1.	PHR_THET8	290-302	1	A:290-302
3	DNA_PHOTOLYASES_1_2	PS00691	DNA photolyases class 1 signature 2.	PHR_THET8	310-329	1	A:310-329

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHR_CRY_ALPHA_BETA	PS51645	Photolyase/cryptochrome alpha/beta domain profile.	PHR_THET8	2-124	2	A:2-124
2	DNA_PHOTOLYASES_1_1	PS00394	DNA photolyases class 1 signature 1.	PHR_THET8	290-302	2	A:290-302
3	DNA_PHOTOLYASES_1_2	PS00691	DNA photolyases class 1 signature 2.	PHR_THET8	310-329	2	A:310-329

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:419
 aligned with PHR_THET8 | P61497 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:419
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411         
            PHR_THET8     2 GPLLVWHRGDLRLHDHPALLEALARGPVVGLVVLDPNNLKTTPRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPYGRYRDGRVREALPVPLHLLPAPHLLPPDLPRAYRVYTPFSRLYRGAAPPLPPPEALPKGPEEGEIPREDPGLPLPEPGEEAALAGLRAFLEAKLPRYAEERDRLDGEGGSRLSPYFALGVLSPRLAAWEAERRGGEGARKWVAELLWRDFSYHLLYHFPWMAERPLDPRFQAFPWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVKHLLLPWKRCEEAFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAPEYPSYAPKDPVVDLEEARRRYLRLARDLARG 420
               SCOP domains d2j08a2 A:2-171 DNA photolyase                                                                                                                                            d2j08a1 A:172-420 C-terminal domain of DNA photolyase                                                                                                                                                                                                     SCOP domains
               CATH domains 2j08A01 A:2-121 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                   2j08A02 A:122-149,A:179-258 -----------------------------2j08A02 A:122-149,A:179-258  [code=1.25.40.80, no name defined]                 2j08A03 A:259-420 DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.........hhhhhhhhh...eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh...eeee...............hhhhhhh....................................hhhhhhhhhhhhhhhh..hhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh......hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhh......hhhhhhhhhh..hhhhhhhh.............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PHR_CRY_ALPHA_BETA  PDB: A:2-124 UniProt: 2-124                                                                            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_PHOTOLYAS-------DNA_PHOTOLYASES_1_2 ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j08 A   2 GPLLVWHRGDLRLHDHPALLEALARGPVVGLVVLDPNNLKTTPRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPYGRYRDGRVREALPVPLHLLPAPHLLPPDLPRAYRVYTPFSRLYRGAAPPLPPPEALPKGPEEGEIPREDPGLPLPEPGEEAALAGLRAFLEAKLPRYAEERDRLDGEGGSRLSPYFALGVLSPRLAAWEAERRGGEGARKWVAELLWRDFSYHLLYHFPWMAERPLDPRFQAFPWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVKHLLLPWKRCEEAFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAPEYPSYAPKDPVVDLEEARRRYLRLARDLARG 420
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (PHR_THET8 | P61497)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003904	deoxyribodipyrimidine photo-lyase activity	Catalysis of the reaction: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA). This reaction represents the reactivation of irradiated DNA by light.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2j08)

Biological Units
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		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	2j08
		Family and Domain Information	:	ProDom \| SYSTERS
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	PHR_THET8 \| P61497
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	4.1.99.3
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)