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(-) Description

Title :  CRYSTAL STRUCTURE OF M. MAZEI PHOTOLYASE SOAKED WITH SYNTHETIC 8-HDF
 
Authors :  S. Kiontke, A. Batschauer, L. -O. Essen
Date :  01 Nov 13  (Deposition) - 21 May 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase, Dna Repair, Antenna Chromophore (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kiontke, P. Gnau, R. Haselsberger, A. Batschauer, L. Essen
Structural And Evolutionary Aspects Of Antenna Chromophore Usage By Class Ii Photolyases.
J. Biol. Chem. V. 289 19659 2014
PubMed-ID: 24849603  |  Reference-DOI: 10.1074/JBC.M113.542431

(-) Compounds

Molecule 1 - DEOXYRIBODIPYRIMIDINE PHOTOLYASE
    Chains: A
    EC Number: 4.1.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 3-464
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 192952
    Strain: GO1
    Synonym: CLASS II CPD PHOTOLYASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FO11Ligand/Ion1-DEOXY-1-(8-HYDROXY-2,4-DIOXO-3,4-DIHYDROPYRIMIDO[4,5-B]QUINOLIN-10(2H)-YL)-D-RIBITOL
3GOL2Ligand/IonGLYCEROL
4SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:252 , LEU A:264 , SER A:265 , ASN A:266 , LEU A:267 , SER A:268 , LEU A:271 , PHE A:298 , GLU A:301 , ILE A:302 , TRP A:305 , LYS A:306 , LYS A:372 , GLY A:375 , ARG A:378 , MET A:379 , ALA A:382 , ASN A:403 , ASP A:409 , GLY A:410 , ASN A:414 , GLY A:415 , SER A:422 , GOL A:1470 , HOH A:2024BINDING SITE FOR RESIDUE FAD A1463
2AC2SOFTWARESER A:26 , ARG A:27 , PHE A:55 , CYS A:56 , THR A:58 , MET A:72 , SER A:118 , LYS A:123 , TRP A:126 , HIS A:272 , PHE A:273 , ARG A:411 , HOH A:2002 , HOH A:2003 , HOH A:2016BINDING SITE FOR RESIDUE FO1 A1464
3AC3SOFTWAREILE A:66 , ARG A:67 , ARG A:215 , ALA A:216 , ARG A:405BINDING SITE FOR RESIDUE SO4 A1465
4AC4SOFTWARELYS A:74 , PRO A:292 , GLY A:293 , LYS A:295 , LYS A:296BINDING SITE FOR RESIDUE SO4 A1466
5AC5SOFTWARELYS A:449 , PHE A:452 , ASP A:453 , VAL A:454 , LYS A:455BINDING SITE FOR RESIDUE SO4 A1467
6AC6SOFTWAREGLN A:77 , GLU A:80 , THR A:199 , LEU A:200 , SER A:201BINDING SITE FOR RESIDUE SO4 A1468
7AC7SOFTWAREALA A:160 , HIS A:161 , ARG A:164BINDING SITE FOR RESIDUE GOL A1469
8AC8SOFTWARETRP A:305 , MET A:379 , TRP A:421 , FAD A:1463BINDING SITE FOR RESIDUE GOL A1470

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CDM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CDM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CDM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CDM)

(-) Exons   (0, 0)

(no "Exon" information available for 4CDM)

(-) 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:454
 aligned with Q8PYK9_METMA | Q8PYK9 from UniProtKB/TrEMBL  Length:464

    Alignment length:462
                                    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  
         Q8PYK9_METMA     1 MIMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEANVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVVPCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPELSAGAGMVETLSDVLETGVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVMESFIADRLDSYGALRNDPTKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYMRMYWAKKILEWSESPEKALEIAICLNDRYELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRKFDVKLYIEKYS 462
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh.eeeee........eeee.........hhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh....eeee......hhhhhh.....hhhhhhhhhhhhhhhhh..............--------.hhhhhhhhhhhhhh....ee...ee..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.........hhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cdm A   1 SHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEANVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVVPCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPE--------ETLSDVLETGVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVMESFIADRLDSYGALRNDPTKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYTRMYWAKKILEWSESPEKALEIAICLNDRYELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRKFDVKLYIEKYS 462
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |-       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  
                                                                                                                                                                                                                      189      198
   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 4CDM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CDM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CDM)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8PYK9_METMA | Q8PYK9)
molecular function
    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.

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 Related Entries

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        Q8PYK9_METMA | Q8PYK9: 2xry 2xrz 4cdn

(-) Related Entries Specified in the PDB File

4cdn CRYSTAL STRUCTURE OF M. MAZEI PHOTOLYASE WITH ITS IN VIVO RECONSTITUTED 8-HDF ANTENNA CHROMOPHORE