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(-) Description

Title :  DROSOPHILA MELANOGASTER (6-4) PHOTOLYASE BOUND TO DOUBLE STRANDED DNA CONTAINING A T(6-4)C PHOTOLESION
 
Authors :  A. F. Glas, S. Schneider, M. J. Maul, U. Hennecke, T. Carell
Date :  20 Feb 09  (Deposition) - 17 Mar 09  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Lyase-Dna Complex, Photolesion, Dna Photolyase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. F. Glas, S. Schneider, M. J. Maul, U. Hennecke, T. Carell
Crystal Structure Of The T(6-4)C Lesion In Complex With A (6-4) Dna Photolyase And Repair Of Uv- Induced (6-4) And Dewar Photolesions.
Chemistry V. 15 10387 2009
PubMed-ID: 19722240  |  Reference-DOI: 10.1002/CHEM.200901004
(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
    Expression System Plasmid: DERIVED FROM PDEST007
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: ROSETTA-GAMI PLYSS (DE3)
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-520
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: DNA PHOTOLYASE, RE11660P
 
Molecule 2 - 5'-D(*AP*CP*AP*GP*CP*GP*GP*64PP*ZP*GP*CP*AP *GP*GP*T)-3'
    Chains: C
    Other Details: 6-4 LINK BETWEEN T 8 AND C 8 (SEE REMARK 600)
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*AP*CP*CP*TP*GP*CP*GP*AP*CP*CP*GP*CP*TP*G)-3'
    Chains: D
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
164P1Mod. Nucleotide5-AMINOTHYMIDINE 5'-(DIHYDROGEN PHOSPHATE)
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3Z1Mod. Residue1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)PYRIMIDIN-2(1H)-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:244 , LYS A:246 , THR A:258 , THR A:259 , VAL A:260 , LEU A:261 , SER A:262 , LEU A:265 , GLN A:299 , ARG A:303 , TYR A:306 , TRP A:362 , HIS A:365 , ARG A:368 , ASP A:397 , ASP A:399 , LEU A:402 , ASN A:403 , ASN A:406 , 64P C:8BINDING SITE FOR RESIDUE FAD A1510

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WB2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:292 -Pro A:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WB2)

(-) Exons   (0, 0)

(no "Exon" information available for 2WB2)

(-) 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:508
 aligned with Q8SXK5_DROME | Q8SXK5 from UniProtKB/TrEMBL  Length:540

    Alignment length:508
                                    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       481       491       501        
         Q8SXK5_DROME     2 DSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREVRTGKE 509
               SCOP domains d2wb2a1 A:2-215 automated matches                                                                                                                                                                                     d2wb2a2 A:216-509 automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------DNA_photolyase-2wb2A01 A:8-184                                                                                                                                                   -------------------------------------FAD_binding_7-2wb2A02 A:222-498                                                                                                                                                                                                                                                      ----------- Pfam domains
         Sec.struct. author ....eeeeeee........hhhhhhhhhhhhhh...eeeeeeeeehhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhheeeeeee...hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhh......hhhhhhhhhh......................hhhhhhh.......hhhhhh.hhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhh...........hhhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....................hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhh..............hhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wb2 A   2 DSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREVRTGKE 509
                                    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       481       491       501        


Chain C from PDB  Type:DNA  Length:15
                                               
                 2wb2 C   1 ACAGCGGtcGCAGGT  15
                                   |10     
                                   8-64P   
                                    9-Z    


Chain D from PDB  Type:DNA  Length:15
                                               
                 2wb2 D   1 TACCTGCGACCGCTG  15
                                    10
   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  (0, 0)

(no "CATH Domain" information available for 2WB2)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8SXK5_DROME | Q8SXK5)
molecular function
    GO:0003914    DNA (6-4) photolyase activity    Catalysis of the reaction: pyrimidine-pyrimidone (6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA). Catalyzes the reactivation of ultraviolet-irradiated DNA.
    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.

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        Q8SXK5_DROME | Q8SXK5: 2wq6 2wq7 3cvu 3cvv 3cvw 3cvx 3cvy

(-) Related Entries Specified in the PDB File

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