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(-) Description

Title :  STRUCTURE OF PHOTOLYASE
 
Authors :  K. Miki, K. Kitadokoro
Date :  04 Jul 97  (Deposition) - 14 Jan 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Repair, Electron Transfer, Excitation Energy Transfer, Lyase (Carbon-Carbon) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tamada, K. Kitadokoro, Y. Higuchi, K. Inaka, A. Yasui, P. E. De Ruiter, A. P. Eker, K. Miki
Crystal Structure Of Dna Photolyase From Anacystis Nidulans
Nat. Struct. Biol. V. 4 887 1997
PubMed-ID: 9360600  |  Reference-DOI: 10.1038/NSB1197-887
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOTOLYASE
    Chains: A
    EC Number: 4.1.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
    Organism Taxid: 269084
    Other Details: PHOTOREACTIVATING ENZYME
    Strain: PCC 6301
    Synonym: DNA CYCLOBUTANE DIPYRIMIDINE PHOTOLYASE

 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
2HDF1Ligand/Ion8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR 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 , TRP A:346 , ASN A:349 , ARG A:352 , ASP A:380 , GLY A:381 , ASP A:382 , ALA A:385 , ASN A:386 , HOH A:578 , HOH A:601 , HOH A:616 , HOH A:631 , HOH A:632 , HOH A:634BINDING SITE FOR RESIDUE FAD A 485
2AC2SOFTWAREARG A:10 , PHE A:35 , CYS A:36 , LEU A:37 , ASP A:38 , ILE A:41 , MET A:47 , ARG A:51 , LEU A:55 , ASP A:101 , GLU A:103 , GLY A:106 , ARG A:109 , LYS A:248 , PHE A:249 , HOH A:635 , HOH A:636 , HOH A:637 , HOH A:647BINDING SITE FOR RESIDUE HDF A 486

(-) SS Bonds  (0, 0)

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

(-) 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 1QNF)

(-) 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 1QNF)

(-) 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:475
 aligned with PHR_SYNP6 | P05327 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:475
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470     
            PHR_SYNP6     1 MAAPILFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLDPQILQSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWRAASAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCWMIVASFLTKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPKPLRIFNPASQAKKFDATATYIKRWLPELRHVHPKDLISGEITPIGRRGYPAPIVNHNLRQKQFKALYNQLKAAI 475
               SCOP domains d1qnfa2 A:1-204 DNA photolyase                                                                                                                                                                              d1qnfa1 A:205-475 C-terminal domain of DNA photolyase                                                                                                                                                                                                                           SCOP domains
               CATH domains --1qnfA01 A:3-129 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                          1qnfA02 A:130-164,A:210-297        ---------------------------------------------1qnfA02 A:130-164,A:210-297  [code=1.25.40.80, no name defined]                         1qnfA03 A:298-473 DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3                                                                                                  -- CATH domains
               Pfam domains ----DNA_photolyase-1qnfA01 A:5-170                                                                                                                                        -------------------------------------FAD_binding_7-1qnfA02 A:208-472                                                                                                                                                                                                                                          --- Pfam domains
         Sec.struct. author ....eeeee.........hhhhhhh.....eeeeeee.hhhh......hhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhh.................hhhhhhhhhh........................hhhhhhhhhhhhhh.hhhhhhhhh..........hhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....hhhhh......hhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhh.......hhhhhhhhhhhh.............hhhhhhhhh...hhhhhh.hhh....hhhhhh....hhhh.........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --PHR_CRY_ALPHA_BETA  PDB: A:3-132 UniProt: 3-132                                                                                   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_PHOTOLYAS-------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qnf A   1 MAAPILFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLDPQILQSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWQAASAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPKPLRIFNPASQAKKFDATATYIKRWLPELRHVHPKDLISGEITPIERRGYPAPIVNHNLRQKQFKALYNQLKAAI 475
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470
   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)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)
(-)
Clan: no clan defined [family: FAD_binding_7] (11)

(-) 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

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        PHR_SYNP6 | P05327: 1owl 1owm 1own 1owo 1owp 1tez

(-) Related Entries Specified in the PDB File

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