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(-) Description

Title :  THERMUS DNA PHOTOLYASE WITH 8-IOD-RIBOFLAVIN ANTENNA CHROMOPHORE
 
Authors :  T. Klar, G. Kaiser, U. Hennecke, T. Carell, A. Batschauer, L. -O. Essen
Date :  01 Aug 06  (Deposition) - 01 May 07  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Lyase, Flavoprotein, Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Klar, G. Kaiser, U. Hennecke, T. Carell, A. Batschauer, L. -O. Essen
Natural And Non-Natural Antenna Chromophores In The Dna Photolyase From Thermus Thermophilus
Chembiochem V. 7 1798 2006
PubMed-ID: 17051659  |  Reference-DOI: 10.1002/CBIC.200600206

(-) Compounds

Molecule 1 - DEOXYRIBODIPYRIMIDINE PHOTO-LYASE
    ChainsA
    EC Number4.1.99.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET36B
    Expression System Vector TypePLASMID
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    Other DetailsGERMAN COLLECTION OF MICROORGANISMS (DSM)
    StrainHB8
    SynonymDNA PHOTOLYASE, PHOTOREACTIVATING ENZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IRF1Ligand/Ion1-DEOXY-1-(8-IODO-7-METHYL-2,4-DIOXO-3,4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL)-D-RIBITOL
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IRF1Ligand/Ion1-DEOXY-1-(8-IODO-7-METHYL-2,4-DIOXO-3,4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL)-D-RIBITOL
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IRF2Ligand/Ion1-DEOXY-1-(8-IODO-7-METHYL-2,4-DIOXO-3,4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL)-D-RIBITOL
4PO44Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:117 , HOH A:2045BINDING SITE FOR RESIDUE CL A 901
2AC2SOFTWAREPRO A:148 , HOH A:2009BINDING SITE FOR RESIDUE CL A 902
3AC3SOFTWAREVAL A:135 , TYR A:136 , THR A:137 , ARG A:167 , ASP A:360 , HOH A:2107 , HOH A:2108BINDING SITE FOR RESIDUE PO4 A1423
4AC4SOFTWARETHR A:42 , ARG A:46 , GLU A:77 , ARG A:336 , HIS A:337BINDING SITE FOR RESIDUE PO4 A1424
5AC5SOFTWARETYR A:197 , SER A:210 , ARG A:211 , LEU A:212 , SER A:213 , PHE A:216 , TRP A:241 , GLU A:244 , LEU A:245 , TRP A:247 , ARG A:248 , PHE A:307 , ASN A:310 , ARG A:313 , ALA A:317 , LEU A:339 , ASP A:341 , GLY A:342 , ASP A:343 , VAL A:346 , ASN A:347 , GLN A:349 , GLY A:350 , HOH A:2089 , HOH A:2096 , HOH A:2101 , HOH A:2102 , HOH A:2103BINDING SITE FOR RESIDUE FAD A1421
6AC6SOFTWAREARG A:9 , GLY A:10 , VAL A:34 , LEU A:35 , ASP A:36 , ASN A:39 , LEU A:40 , PHE A:50 , SER A:96 , ARG A:104 , LEU A:218 , GLY A:342 , HOH A:2104 , HOH A:2105 , HOH A:2106BINDING SITE FOR RESIDUE IRF A1422

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J08)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHR_CRY_ALPHA_BETAPS51645 Photolyase/cryptochrome alpha/beta domain profile.PHR_THET82-124  1A:2-124
2DNA_PHOTOLYASES_1_1PS00394 DNA photolyases class 1 signature 1.PHR_THET8290-302  1A:290-302
3DNA_PHOTOLYASES_1_2PS00691 DNA photolyases class 1 signature 2.PHR_THET8310-329  1A:310-329
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHR_CRY_ALPHA_BETAPS51645 Photolyase/cryptochrome alpha/beta domain profile.PHR_THET82-124  1A:2-124
2DNA_PHOTOLYASES_1_1PS00394 DNA photolyases class 1 signature 1.PHR_THET8290-302  1A:290-302
3DNA_PHOTOLYASES_1_2PS00691 DNA photolyases class 1 signature 2.PHR_THET8310-329  1A:310-329
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHR_CRY_ALPHA_BETAPS51645 Photolyase/cryptochrome alpha/beta domain profile.PHR_THET82-124  2A:2-124
2DNA_PHOTOLYASES_1_1PS00394 DNA photolyases class 1 signature 1.PHR_THET8290-302  2A:290-302
3DNA_PHOTOLYASES_1_2PS00691 DNA photolyases class 1 signature 2.PHR_THET8310-329  2A:310-329

(-) Exons   (0, 0)

(no "Exon" information available for 2J08)

(-) Sequences/Alignments

Asymmetric 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:419
 aligned with PHR_THET8 | P61497 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:419
                                    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         
            PHR_THET8     2 GPLLVWHRGDLRLHDHPALLEALARGPVVGLVVLDPNNLKTTPRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPYGRYRDGRVREALPVPLHLLPAPHLLPPDLPRAYRVYTPFSRLYRGAAPPLPPPEALPKGPEEGEIPREDPGLPLPEPGEEAALAGLRAFLEAKLPRYAEERDRLDGEGGSRLSPYFALGVLSPRLAAWEAERRGGEGARKWVAELLWRDFSYHLLYHFPWMAERPLDPRFQAFPWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVKHLLLPWKRCEEAFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAPEYPSYAPKDPVVDLEEARRRYLRLARDLARG 420
               SCOP domains d2j08a2 A:2-171 DNA photolyase                                                                                                                                            d2j08a1 A:172-420 C-terminal domain of DNA photolyase                                                                                                                                                                                                     SCOP domains
               CATH domains 2j08A01 A:2-121 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                   2j08A02 A:122-149,A:179-258 -----------------------------2j08A02 A:122-149,A:179-258  [code=1.25.40.80, no name defined]                 2j08A03 A:259-420 DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.........hhhhhhhhh...eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh...eeee...............hhhhhhh....................................hhhhhhhhhhhhhhhh..hhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh......hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhh......hhhhhhhhhh..hhhhhhhh.............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PHR_CRY_ALPHA_BETA  PDB: A:2-124 UniProt: 2-124                                                                            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_PHOTOLYAS-------DNA_PHOTOLYASES_1_2 ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j08 A   2 GPLLVWHRGDLRLHDHPALLEALARGPVVGLVVLDPNNLKTTPRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPYGRYRDGRVREALPVPLHLLPAPHLLPPDLPRAYRVYTPFSRLYRGAAPPLPPPEALPKGPEEGEIPREDPGLPLPEPGEEAALAGLRAFLEAKLPRYAEERDRLDGEGGSRLSPYFALGVLSPRLAAWEAERRGGEGARKWVAELLWRDFSYHLLYHFPWMAERPLDPRFQAFPWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVKHLLLPWKRCEEAFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAPEYPSYAPKDPVVDLEEARRRYLRLARDLARG 420
                                    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         

   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 Unit

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J08)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (PHR_THET8 | P61497)
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_THET8 | P614971iqr 1iqu 2j07 2j09

(-) Related Entries Specified in the PDB File

1iqr CRYSTAL STRUCTURE OF DNA PHOTOLYASE FROM THERMUSTHERMOPHILUS
1iqu CRYSTAL STRUCTURE OF PHOTOLYASE-THYMINE COMPLEX
2cgb THERMUS DNA PHOTOLYASE WITH FMN ANTENNA CHROMOPHORE
2cgc THERMUS DNA PHOTOLYASE WITH 8-HDF ANTENNA CHROMOPHORE
2j07 THERMUS DNA PHOTOLYASE WITH 8-HDF ANTENNA CHROMOPHORE
2j09 THERMUS DNA PHOTOLYASE WITH FMN CHROMOPHORE