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(-) Description

Title :  XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE
 
Authors :  J. E. A. Wibley, L. H. Pearl
Date :  19 Mar 03  (Deposition) - 11 Jul 03  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,E,F
Keywords :  Hydrolase-Dna Complex, Dna Glycosylase, Single Stranded (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. A. Wibley, T. R. Waters, K. Haushalter, G. L. Verdine, L. H. Pearl
Structure And Specificity Of The Vertebrate Anti-Mutator Uracil-Dna Glycosylase Smug1
Mol. Cell V. 11 1647 2003
PubMed-ID: 12820976  |  Reference-DOI: 10.1016/S1097-2765(03)00235-1

(-) Compounds

Molecule 1 - SINGLE-STRAND SELECTIVE MONOFUNCTIONAL URACIL DNA GLYCOSYLASE
    Chains: A, B
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1-247
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: SMUG1
 
Molecule 2 - 5'-D(*CP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*G)-3'
    Chains: E
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*3DRP*GP*GP*AP*CP*TP*3DRP*AP*CP*GP*GP*GP)-3'
    Chains: F
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
13DR2Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2DUR1Ligand/Ion2'-DEOXYURIDINE
3EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
4GOL1Ligand/IonGLYCEROL
5IPA2Ligand/IonISOPROPYL ALCOHOL
6URA1Ligand/IonURACIL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:94 , MET A:95 , ASN A:96 , GLY A:98 , PHE A:109 , ASN A:174 , HIS A:250 , HOH A:2031 , HOH A:2035 , HOH A:2120BINDING SITE FOR RESIDUE URA A1282
2AC2SOFTWARESER A:54 , TYR A:66 , ASN A:67 , TYR A:71 , PRO A:128 , GLU A:129 , HOH A:2049 , HOH A:2123BINDING SITE FOR RESIDUE EPE A1285
3AC3SOFTWARESER B:54 , TYR B:66 , ASN B:67 , TYR B:71 , PRO B:128 , GLU B:129 , HOH B:2082BINDING SITE FOR RESIDUE EPE B1282
4AC4SOFTWAREASN B:96 , PHE B:109 , GLU B:146 , SER B:148 , HIS B:250 , SER B:252 , HOH B:2017 , DC F:392 , 3DR F:393 , DG F:394BINDING SITE FOR RESIDUE DUR F1405
5AC5SOFTWAREPRO A:99 , GLU A:146 , HOH A:2099 , HOH A:2119 , HOH A:2120BINDING SITE FOR RESIDUE GOL A1283
6AC6SOFTWAREASP A:117 , HOH A:2122 , ARG B:151BINDING SITE FOR RESIDUE IPA A1284
7AC7SOFTWAREALA A:150 , ARG A:151 , SER A:154 , ASN B:113 , ASP B:117 , HOH B:2081BINDING SITE FOR RESIDUE IPA B1281

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OE5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OE5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OE5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OE5)

(-) Exons   (0, 0)

(no "Exon" information available for 1OE5)

(-) 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:244
 aligned with SMUG1_XENLA | Q9YGN6 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:244
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276    
          SMUG1_XENLA    37 SPADSFLKVELELNLKLSNLVFQDPVQYVYNPLVYAWAPHENYVQTYCKSKKEVLFLGMNPGPFGMAQTGVPFGEVNHVRDWLQIEGPVSKPEVEHPKRRIRGFECPQSEVSGARFWSLFKSLCGQPETFFKHCFVHNHCPLIFMNHSGKNLTPTDLPKAQRDTLLEICDEALCQAVRVLGVKLVIGVGRFSEQRARKALMAEGIDVTVKGIMHPSPRNPQANKGWEGIVRGQLLELGVLSLLT 280
               SCOP domains d1oe5a_ A: Single-strand selective monofunctional uracil-DNA glycosylase SMUG1                                                                                                                                                                       SCOP domains
               CATH domains 1oe5A00 A:37-280 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh........eeehhhhhhhhhhhhhhhhhh.....eeeee......hhhhhh....hhhhhhhh...................hhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eeeee....eee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhh....eeeee............hhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oe5 A  37 SPADSFLKVELELNLKLSNLVFQDPVQYVYNPLVYAWAPHENYVQTYCKSKKEVLFLGMNPGPFGMAQTGVPFGEVNHVRDWLQIEGPVSKPEVEHPKRRIRGFECPQSEVSGARFWSLFKSLCGQPETFFKHCFVHNHCPLIFMNHSGKNLTPTDLPKAQRDTLLEICDEALCQAVRVLGVKLVIGVGRFSEQRARKALMAEGIDVTVKGIMHPSPRNPQANKGWEGIVRGQLLELGVLSLLT 280
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276    


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with SMUG1_XENLA | Q9YGN6 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:245
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275     
          SMUG1_XENLA    36 ESPADSFLKVELELNLKLSNLVFQDPVQYVYNPLVYAWAPHENYVQTYCKSKKEVLFLGMNPGPFGMAQTGVPFGEVNHVRDWLQIEGPVSKPEVEHPKRRIRGFECPQSEVSGARFWSLFKSLCGQPETFFKHCFVHNHCPLIFMNHSGKNLTPTDLPKAQRDTLLEICDEALCQAVRVLGVKLVIGVGRFSEQRARKALMAEGIDVTVKGIMHPSPRNPQANKGWEGIVRGQLLELGVLSLLT 280
               SCOP domains d1oe5b_ B: Single-strand selective monofunctional uracil-DNA glycosylase SMUG1                                                                                                                                                                        SCOP domains
               CATH domains 1oe5B00 B:36-280 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh........eeehhhhhhhhhhhhhhhhhh.....eeeee......hhhhhh....hhhhhhhh.............hhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eeeee....eee.....eehhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oe5 B  36 ESPADSFLKVELELNLKLSNLVFQDPVQYVYNPLVYAWAPHENYVQTYCKSKKEVLFLGMNPGPFGMAQTGVPFGEVNHVRDWLQIEGPVSKPEVEHPKRRIRGFECPQSEVSGARFWSLFKSLCGQPETFFKHCFVHNHCPLIFMNHSGKNLTPTDLPKAQRDTLLEICDEALCQAVRVLGVKLVIGVGRFSEQRARKALMAEGIDVTVKGIMHPSPRNPQANKGWEGIVRGQLLELGVLSLLT 280
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275     


Chain E from PDB  Type:DNA  Length:12
                                            
                 1oe5 E 281 CCCGTGAGTCCG 292
                                   290  


Chain F from PDB  Type:DNA  Length:13
                                             
                 1oe5 F 392 CxGGACTxACGGG 404
                             |     401   
                           393-3DR |     
                                 399-3DR
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OE5)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SMUG1_XENLA | Q9YGN6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        SMUG1_XENLA | Q9YGN6: 1oe4 1oe6

(-) Related Entries Specified in the PDB File

1oe4 XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE
1oe6 XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE