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(-) Description

Title :  X-RAY STRUCTURE OF ARCHAEAL CLASS II CPD PHOTOLYASE FROM METHANOSARCINA MAZEI
 
Authors :  S. Kiontke, Y. Geisselbrecht, R. Pokorny, T. Carell, A. Batschauer, L.
Date :  24 Sep 10  (Deposition) - 14 Sep 11  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Damage, Dna Repair, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kiontke, Y. Geisselbrecht, R. Pokorny, T. Carell, A. Batschauer, L. O. Essen
Crystal Structures Of An Archaeal Class Ii Dna Photolyase And Its Complex With Uv-Damaged Duplex Dna.
Embo J. V. 30 4437 2011
PubMed-ID: 21892138  |  Reference-DOI: 10.1038/EMBOJ.2011.313

(-) 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
    Mutation: YES
    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  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL2Ligand/IonGLYCEROL
3SO49Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR 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 , SER A:309 , 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:1474 , HOH A:2084 , HOH A:2354 , HOH A:2355 , HOH A:2356 , HOH A:2357 , HOH A:2375BINDING SITE FOR RESIDUE FAD A1463
02AC2SOFTWAREGLY A:65 , ILE A:66 , ARG A:67 , ARG A:215 , ALA A:216 , PHE A:225 , ARG A:405 , HOH A:2179 , HOH A:2358 , HOH A:2359BINDING SITE FOR RESIDUE SO4 A1464
03AC3SOFTWAREALA A:160 , HIS A:161 , ARG A:164 , HOH A:2325 , HOH A:2360BINDING SITE FOR RESIDUE SO4 A1465
04AC4SOFTWARELYS A:129 , HIS A:156 , TYR A:158 , PRO A:326 , HOH A:2151 , HOH A:2265 , HOH A:2361 , HOH A:2362 , HOH A:2363 , HOH A:2366BINDING SITE FOR RESIDUE SO4 A1466
05AC5SOFTWAREGLN A:77 , GLU A:80 , LEU A:200 , SER A:201 , HOH A:2072 , HOH A:2077BINDING SITE FOR RESIDUE SO4 A1467
06AC6SOFTWARELYS A:449 , PHE A:452 , ASP A:453 , VAL A:454 , LYS A:455BINDING SITE FOR RESIDUE SO4 A1468
07AC7SOFTWARELYS A:74 , PRO A:292 , GLY A:293 , SER A:294 , LYS A:295 , LYS A:296 , HOH A:2071 , HOH A:2242 , HOH A:2365BINDING SITE FOR RESIDUE SO4 A1469
08AC8SOFTWAREASP A:96 , GLY A:98 , GLU A:99 , SER A:327 , LYS A:330 , HOH A:2362 , HOH A:2366 , HOH A:2367 , HOH A:2368BINDING SITE FOR RESIDUE SO4 A1470
09AC9SOFTWARESER A:153 , GLN A:154 , LYS A:166 , HOH A:2143 , HOH A:2369BINDING SITE FOR RESIDUE SO4 A1471
10BC1SOFTWARESER A:26 , ARG A:27 , SER A:118 , HOH A:2118 , HOH A:2231 , HOH A:2370 , HOH A:2371BINDING SITE FOR RESIDUE SO4 A1472
11BC2SOFTWAREARG A:121 , ILE A:122 , TYR A:319 , ASP A:320 , TYR A:416 , HOH A:2322 , HOH A:2372 , HOH A:2373BINDING SITE FOR RESIDUE GOL A1473
12BC3SOFTWARETRP A:305 , MET A:379 , GLY A:418 , TRP A:421 , FAD A:1463 , HOH A:2374 , HOH A:2375BINDING SITE FOR RESIDUE GOL A1474

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XRY)

(-) 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:458
 aligned with Q8PYK9_METMA | Q8PYK9 from UniProtKB/TrEMBL  Length:464

    Alignment length:467
                                 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       
         Q8PYK9_METMA     - -----MIMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEANVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVVPCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPELSAGAGMVETLSDVLETGVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVMESFIADRLDSYGALRNDPTKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYMRMYWAKKILEWSESPEKALEIAICLNDRYELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRKFDVKLYIEKYS 462
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhheeeee........eeee..........hhhhhhhhhhhhh...eeeeeee...hhh..hhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh...eeee.....hhhhhhhhhhhh.....eeee.......hhhh.......hhhhhhhhhhhhhhh..............---------..hhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhh..hhhhhhhhhh..........hhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh......hhhhhhhhhhhh....................hhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xry A  -4 LVPRGSHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEANVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVVPCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTP---------ETLSDVLETGVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVMESFIADRLDSYGALRNDPTKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYTRMYWAKKILEWSESPEKALEIAICLNDRYELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRKFDVKLYIEKYS 462
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185  |      -  |    205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       
                                                                                                                                                                                                                          188       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 2XRY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8PYK9_METMA | Q8PYK9: 2xrz 4cdm 4cdn

(-) Related Entries Specified in the PDB File

2xrz X-RAY STRUCTURE OF ARCHAEAL CLASS II CPD PHOTOLYASE FROM METHANOSARCINA MAZEI IN COMPLEX WITH INTACT CPD-LESION