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(-) Description

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)

(-) Compounds

Molecule 1 - DEOXYRIBODIPYRIMIDINE PHOTOLYASE
    ChainsA
    EC Number4.1.99.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificSYNECHOCOCCUS ELONGATUS
    Organism Taxid269084
    StrainPCC 6301
    SynonymPHOTOLYASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:11 , ILE A:41 , MET A:47 , ARG A:51 , LYS A:248 , PHE A:249 , HOH A:689 , HOH A:690BINDING SITE FOR RESIDUE PO4 A 486
2AC2SOFTWARETYR 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:681BINDING SITE FOR RESIDUE FAD A 485

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:229 -Pro A:230

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHR_CRY_ALPHA_BETAPS51645 Photolyase/cryptochrome alpha/beta domain profile.PHR_SYNP63-132  1A:3-132
2DNA_PHOTOLYASES_1_1PS00394 DNA photolyases class 1 signature 1.PHR_SYNP6329-341  1A:329-341

(-) Exons   (0, 0)

(no "Exon" information available for 1OWM)

(-) Sequences/Alignments

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)
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  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)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PHR_SYNP6 | P053271owl 1own 1owo 1owp 1qnf 1tez

(-) Related Entries Specified in the PDB File

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).