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(-) Description

Title :  DROSOPHILA MELANOGASTER (6-4) PHOTOLYASE H365N MUTANT BOUND TO DS DNA WITH A T-T (6-4) PHOTOLESION AND COFACTOR F0
 
Authors :  M. J. Maul, T. R. M. Barends, A. F. Glas, M. J. Cryle, I. Schlichting, T. Carell
Date :  20 Apr 08  (Deposition) - 13 Oct 09  (Release) - 13 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Dna Repair, Lyase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Maul, T. Barends, A. F. Glas, M. J. Cryle, S. Schneider, T. Domratcheva, I. Schlichting, T. Carell
Structure And Mechanism Of A Cofactor F0 Accelerated (6-4) Photolyase From The Fruit Fly
To Be Published
PubMed: search
(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
    Mutation: YES
    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  (4, 4)

Asymmetric/Biological Unit (4, 4)
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
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4FO11Ligand/Ion1-DEOXY-1-(8-HYDROXY-2,4-DIOXO-3,4-DIHYDROPYRIMIDO[4,5-B]QUINOLIN-10(2H)-YL)-D-RIBITOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:244 , LYS A:246 , THR A:258 , THR A:259 , LEU A:261 , SER A:262 , LEU A:265 , GLN A:299 , TRP A:302 , ARG A:303 , TYR A:306 , TRP A:362 , ASN A:365 , ARG A:368 , HIS A:369 , ASP A:397 , GLN A:398 , ASP A:399 , LEU A:402 , ASN A:403 , ASN A:406 , TRP A:407BINDING SITE FOR RESIDUE FAD A 521
2AC2SOFTWAREARG A:13 , LYS A:14 , PHE A:44 , ILE A:45 , LEU A:46 , ASP A:47 , ILE A:50 , MET A:54 , ARG A:60 , ASP A:110 , GLU A:112 , ARG A:118 , LYS A:266BINDING SITE FOR RESIDUE FO1 A 1422

(-) SS Bonds  (0, 0)

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

(-) 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 3CVW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CVW)

(-) 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:502
 aligned with Q8SXK5_DROME | Q8SXK5 from UniProtKB/TrEMBL  Length:540

    Alignment length:502
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503  
         Q8SXK5_DROME     4 QRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREVR 505
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee........hhhhhhhhhhhhhh...eeeeeeeee..hhhhhh..hhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhhhh..ee.........hhhhhhhhh......hhhhhhhhhh......................hhhhhhh.......hhhhhh.hhhhh.......hhhhhhhhhhhhh.hhhhhhh.hhhhh...........hhhhhhh...hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh...................hhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhh........................hhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvw A   4 QRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHNLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREVR 505
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503  


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


Chain D from PDB  Type:DNA  Length:15
                                               
                 3cvw 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  (0, 0)

(no "SCOP Domain" information available for 3CVW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CVW)

(-) Pfam Domains  (0, 0)

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

(-) 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 Specified in the PDB File

3cvu DROSOPHILA MELANOGASTER (6-4) PHOTOLYASE BOUND TO DS DNA WITH A T-T (6-4) PHOTOLESION
3cvv DROSOPHILA MELANOGASTER (6-4) PHOTOLYASE BOUND TO DS DNA WITH A T-T (6-4) PHOTOLESION AND F0 COFACTOR
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