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(-) Description

Title :  CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM ATLANTIC COD (GADUS MORHUA)
 
Authors :  I. Leiros, E. Moe, O. Lanes, A. O. Smalas, N. P. Willassen
Date :  21 Jul 03  (Deposition) - 05 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Uracil-Dna Glycosylase, Crystal Structure, Cold-Adaptation, Base Excision Repair, Structure-Function Relationship (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Leiros, E. Moe, O. Lanes, A. O. Smalas, N. P. Willassen
The Crystal Structure Of Uracil-Dna Glycosylase From Atlantic Cod (Gadus Morhua) Reveals Cold-Adaptation Features
Acta Crystallogr. , Sect. D V. 59 1357 2003
PubMed-ID: 12876336  |  Reference-DOI: 10.1107/S0907444903011144

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    ChainsA, B
    EC Number3.2.2.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN, RESIDUES 79-301
    MutationYES
    OrganLIVER
    Organism CommonATLANTIC COD
    Organism ScientificGADUS MORHUA
    Organism Taxid8049

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:113 , VAL A:118 , HOH A:2024 , HOH A:2025BINDING SITE FOR RESIDUE CL A1306
2AC2SOFTWAREARG B:113 , VAL B:118 , HOH B:2023 , HOH B:2027BINDING SITE FOR RESIDUE CL B1306
3AC3SOFTWAREGLN A:144 , ASP A:145 , CYS A:157 , PHE A:158 , ASN A:204 , HIS A:268 , HOH A:2075 , HOH A:2178BINDING SITE FOR RESIDUE GOL A1305
4AC4SOFTWAREGLN B:144 , ASP B:145 , CYS B:157 , PHE B:158 , ASN B:204 , HIS B:268BINDING SITE FOR RESIDUE GOL B1305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OKB)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:119 -Pro A:120
2Lys A:162 -Pro A:163
3Tyr B:119 -Pro B:120
4Lys B:162 -Pro B:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OKB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OKB)

(-) Exons   (0, 0)

(no "Exon" information available for 1OKB)

(-) 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:223
 aligned with Q9I983_GADMO | Q9I983 from UniProtKB/TrEMBL  Length:301

    Alignment length:269
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292         
         Q9I983_GADMO    33 MKITPKKLRSSNVEQKTSSPQLSVEQLERMAKNKKAALDKIRAKATPAGFGETWRRELAAEFEKPYFKQLMSFVADERSRHTVYPPADQVYSWTEMCDIQDVKVVILGQDPYHGPNQAHGLCFSVQKPVPPPPSLVNIYKELCTDIDGFKHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKDRGWETFTDAVIKWLSVNREGVVFLLWGSYAHKKGATIDRKRHHVLQAVHPSPLSAHRGFLGCKHFSKANGLLKLSGTEPINWRAL 301
               SCOP domains d1o                                              kba_ A: Uracil-DNA glycosylase                                                                                                                                                                                               SCOP domains
               CATH domains 1ok                                              bA00 A:82-304 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhh..hhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh.....eeeee......hhhhh....hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1okb A  82 MEF----------------------------------------------FGETWRRELAAEFEKPYFKQLMSFVADERSRHTVYPPADQVYSWTEMCDIQDVKVVILGQDPYHGPNQAHGLCFSVQKPVPPPPSLVNIYKELCTDIDGFKHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKDRGWETFTDAVIKWLSVNREGVVFLLWGSYAHKKGATIDRKRHHVLQAVHPSPLSAHRGFLGCKHFSKANGLLKLSGTEPINWRAL 304
                              |      -         -         -         -        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295         
                             84                                             85                                                                                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:223
 aligned with Q9I983_GADMO | Q9I983 from UniProtKB/TrEMBL  Length:301

    Alignment length:269
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292         
         Q9I983_GADMO    33 MKITPKKLRSSNVEQKTSSPQLSVEQLERMAKNKKAALDKIRAKATPAGFGETWRRELAAEFEKPYFKQLMSFVADERSRHTVYPPADQVYSWTEMCDIQDVKVVILGQDPYHGPNQAHGLCFSVQKPVPPPPSLVNIYKELCTDIDGFKHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKDRGWETFTDAVIKWLSVNREGVVFLLWGSYAHKKGATIDRKRHHVLQAVHPSPLSAHRGFLGCKHFSKANGLLKLSGTEPINWRAL 301
               SCOP domains d1o                                              kbb_ B: Uracil-DNA glycosylase                                                                                                                                                                                               SCOP domains
               CATH domains 1ok                                              bB00 B:82-304 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                              CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------UDG-1okbB01 B:131-292                                                                                                                                             ------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------UDG-1okbB02 B:131-292                                                                                                                                             ------------ Pfam domains (2)
         Sec.struct. author ...----------------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhh..hhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh.....eeeee......hhhhh....hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1okb B  82 MEF----------------------------------------------FGETWRRELAAEFEKPYFKQLMSFVADERSRHTVYPPADQVYSWTEMCDIQDVKVVILGQDPYHGPNQAHGLCFSVQKPVPPPPSLVNIYKELCTDIDGFKHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKDRGWETFTDAVIKWLSVNREGVVFLLWGSYAHKKGATIDRKRHHVLQAVHPSPLSAHRGFLGCKHFSKANGLLKLSGTEPINWRAL 304
                              |      -         -         -         -        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295         
                             84                                             85                                                                                                                                                                                                                           

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9I983_GADMO | Q9I983)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0004844    uracil DNA N-glycosylase activity    Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.
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:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        Q9I983_GADMO | Q9I9834lyl

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