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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   DATA1:DNA PHOTOLYASE / RECEIVED X-RAYS DOSE 1.2 EXP15 PHOTONS/MM2

Authors :   H. Komori, S. Adachi, K. Miki, A. Eker, R. Kort

Date :   28 Mar 03 (Deposition) - 13 Apr 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Dna Repair, Flavin Enzyme, Photoreactivating Enzyme, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Kort, H. Komori, S. Adachi, K. Miki, A. Eker
Dna Apophotolyase From Anacystis Nidulans: 1. 8 A Structure, 8-Hdf Reconstitution And X-Ray-Induced Fad Reduction.
Acta Crystallogr. , Sect. D V. 60 1205 2004
PubMed-ID: 15213381 | Reference-DOI: 10.1107/S0907444904009321
(for further references see the PDB file header)

Molecule 1 - DEOXYRIBODIPYRIMIDINE PHOTOLYASE
	Chains	:	A
	EC Number	:	4.1.99.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SYNECHOCOCCUS ELONGATUS
	Organism Taxid	:	269084
	Strain	:	PCC 6301
	Synonym	:	PHOTOLYASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:11 , ILE A:41 , MET A:47 , ARG A:51 , LYS A:248 , PHE A:249 , HOH A:689 , HOH A:690	BINDING SITE FOR RESIDUE PO4 A 486
2	AC2	SOFTWARE	TYR A:228 , THR A:240 , SER A:241 , GLY A:242 , LEU A:243 , SER A:244 , LEU A:247 , TRP A:280 , GLU A:283 , ARG A:287 , TYR A:290 , TRP A:346 , MET A:347 , ASN A:349 , ARG A:352 , MET A:353 , PHE A:374 , LEU A:378 , ASP A:380 , GLY A:381 , ASP A:382 , ALA A:385 , ASN A:386 , GLY A:389 , TRP A:390 , HOH A:514 , HOH A:524 , HOH A:592 , HOH A:636 , HOH A:643 , HOH A:681	BINDING SITE FOR RESIDUE FAD A 485

(no "SS Bond" information available for 1OWM)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:229	-	Pro A:230

(no "SAP(SNP)/Variant" information available for 1OWM)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHR_CRY_ALPHA_BETA	PS51645	Photolyase/cryptochrome alpha/beta domain profile.	PHR_SYNP6	3-132	1	A:3-132
2	DNA_PHOTOLYASES_1_1	PS00394	DNA photolyases class 1 signature 1.	PHR_SYNP6	329-341	1	A:329-341

(no "Exon" information available for 1OWM)

Asymmetric/Biological 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:474
 aligned with PHR_SYNP6 | P05327 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:474
                                    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       421       431       441       451       461       471    
            PHR_SYNP6     2 AAPILFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLDPQILQSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWRAASAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCWMIVASFLTKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPKPLRIFNPASQAKKFDATATYIKRWLPELRHVHPKDLISGEITPIGRRGYPAPIVNHNLRQKQFKALYNQLKAAI 475
               SCOP domains d1owma2 A:2-204 DNA photolyase                                                                                                                                                                             d1owma1 A:205-475 C-terminal domain of DNA photolyase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1owmA01 A:2-129 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                           1owmA02 A:130-164,A:210-297        ---------------------------------------------1owmA02 A:130-164,A:210-297  [code=1.25.40.80, no name defined]                         1owmA03 A:298-473 DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3                                                                                                  -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee........hhhhhhhhh....eeeeeeehhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh..eeeee....................hhhhhhhhhhhh...............hhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhh.............hhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhh..hhhhhh.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -PHR_CRY_ALPHA_BETA  PDB: A:3-132 UniProt: 3-132                                                                                   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_PHOTOLYAS-------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1owm A   2 AAPILFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLDPQILQSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWQAASAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPKPLRIFNPASQAKKFDATATYIKRWLPELRHVHPKDLISGEITPIERRGYPAPIVNHNLRQKQFKALYNQLKAAI 475
                                    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       421       431       441       451       461       471

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 '\|'

(no "Pfam Domain" information available for 1OWM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PHR_SYNP6 | P05327)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:229 - Pro A:230	[ RasMol ]

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	1owm
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	4.1.99.3
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UniProtKB/Swiss-Prot
	PHR_SYNP6 \| P05327	:	1owl 1own 1owo 1owp 1qnf 1tez

1owl	STRUCTURE OF APOPHOTOLYASE FROM ANACYSTIS NIDULANS.
1own	THE SAME PROTEIN WITHOUT 2-MERCAPTOETHANOL (DATA3).
1owo	THE SAME PROTEIN WITH 2-MERCAPTOETHANOL (DATA4).
1owp	THE SAME PROTEIN WITH 2-MERCAPTOETHANOL (DATA6).
1qnf	THE SAME PROTEIN WITHOUT A LIGHT-HARVESTING COFACTOR (8- HDF).

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (0, 0)

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Gene Ontology (7, 7)

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