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(-) Description

Title :  DROSOPHILA MELANOGASTER (6-4) PHOTOLYASE BOUND TO DS DNA WITH A T-T (6-4) PHOTOLESION AND F0 COFACTOR
 
Authors :  A. F. Glas, M. J. Maul, M. J. Cryle, T. R. M. Barends, S. Schneider, E. Kaya, I. Schlichting, T. Carell
Date :  20 Apr 08  (Deposition) - 16 Jun 09  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Dna Repair, Lyase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. F. Glas, M. J. Maul, M. Cryle, T. R. Barends, S. Schneider, E. Kaya, I. Schlichting, T. Carell
The Archaeal Cofactor F0 Is A Light-Harvesting Antenna Chromophore In Eukaryotes.
Proc. Natl. Acad. Sci. Usa V. 106 11540 2009
PubMed-ID: 19570997  |  Reference-DOI: 10.1073/PNAS.0812665106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RE11660P
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: DERIVED FROM PDEST007
    Expression System Strain: ROSETTA-GAMI PLYSS (DE-3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PHR64-520
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
 
Molecule 2 - DNA (5'-D(*DAP*DCP*DAP*DGP*DCP*DGP*DGP*(64T) P*(5PY)P*DGP*DCP*DAP*DGP*DGP*DT)-3')
    Chains: C
    Engineered: YES
    Other Details: DNA WITH (6-4) PHOTOLESION
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*DTP*DAP*DCP*DCP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DCP*DTP* DG)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
15PY1Mod. Nucleotide1-(2'-DEOXY-5'-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-METHYLPYRIMIDIN-2(1H)-ONE
264T1Mod. Nucleotide5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE
3EDO4Ligand/Ion1,2-ETHANEDIOL
4FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
5FO11Ligand/Ion1-DEOXY-1-(8-HYDROXY-2,4-DIOXO-3,4-DIHYDROPYRIMIDO[4,5-B]QUINOLIN-10(2H)-YL)-D-RIBITOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
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 , HIS A:369 , PHE A:391 , LEU A:395 , ASP A:397 , GLN A:398 , ASP A:399 , LEU A:402 , ASN A:403 , ASN A:406 , TRP A:407 , HOH A:581 , HOH A:662 , 64T C:8BINDING SITE FOR RESIDUE FAD A 521
2AC2SOFTWAREARG A:13 , PHE A:44 , ILE A:45 , LEU A:46 , ASP A:47 , ARG A:60 , ASP A:110 , GLU A:112 , TYR A:114 , SER A:115 , ARG A:118 , LYS A:266 , GLN A:398 , HOH A:533 , HOH A:570 , HOH A:584 , HOH A:702 , HOH A:886BINDING SITE FOR RESIDUE FO1 A 522
3AC3SOFTWARETRP A:458 , LYS A:459 , ARG A:479 , GLU A:484 , HOH A:642 , HOH D:475BINDING SITE FOR RESIDUE EDO A 523
4AC4SOFTWARELYS A:189 , HIS A:437 , LYS A:441 , HOH A:907BINDING SITE FOR RESIDUE EDO A 524
5AC5SOFTWAREDG C:10 , HOH C:51 , DG D:6 , DC D:7BINDING SITE FOR RESIDUE EDO C 16
6AC6SOFTWAREGLN A:418 , TYR A:419 , PHE A:420 , DA D:9 , DC D:10BINDING SITE FOR RESIDUE EDO D 16

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CVV)

(-) 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 3CVV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CVV)

(-) Exons   (0, 0)

(no "Exon" information available for 3CVV)

(-) 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:519
 aligned with Q8SXK5_DROME | Q8SXK5 from UniProtKB/TrEMBL  Length:540

    Alignment length:519
                                          1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                     -    |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496         
         Q8SXK5_DROME     - --------------MDSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREVR 505
               SCOP domains d3cvva1 A:-13-215 automated matches                                                                                                                                                                                                  d3cvva2 A:216-505 automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhheeeeeee........hhhhhhhhhhhhhh...eeeeeeeee..hhhhhh..hhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhh......hhhhhhhhhh......................hhhhhhh.......hhhhhh.hhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhh...........hhhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.....................hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhh...............hhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvv A -13 EKGASTSLYKKAGLMDSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREVR 505
                                    -4         6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496         


Chain C from PDB  Type:DNA  Length:15
                                               
                 3cvv C   1 ACAGCGGttGCAGGT  15
                                   |10     
                                   8-64T   
                                    9-5PY  


Chain D from PDB  Type:DNA  Length:15
                                               
                 3cvv D   1 TACCTGCAACCGCTG  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 3CVV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CVV)

(-) 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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 Related Entries

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        Q8SXK5_DROME | Q8SXK5: 2wb2 2wq6 2wq7 3cvu 3cvw 3cvx 3cvy

(-) Related Entries Specified in the PDB File

3cvu DROSOPHILA MELANOGASTER (6-4) PHOTOLYASE BOUND TO DS DNA WITH A T-T (6-4) PHOTOLESION
3cvw DROSOPHILA MELANOGASTER (6-4) PHOTOLYASE H365N MUTANT BOUND TO DS DNA WITH A T-T (6-4) PHOTOLESION AND COFACTOR F0
3cvx DROSOPHILA MELANOGASTER (6-4) PHOTOLYASE H369M MUTANT BOUND TO DS DNA WITH A T-T (6-4) PHOTOLESION
3cvy DROSOPHILA MELANOGASTER (6-4) PHOTOLYASE BOUND TO REPAIRED DS DNA