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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 :  2.00
Chains :  Asym./Biol. Unit :  A,B,E,F
Keywords :  Hydrolase-Dna Complex, Hydrolase, 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*GP*GP*AP*CP*TP*3DR*AP*CP*GP*GP*G)-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  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2GOL6Ligand/IonGLYCEROL
3IPA1Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:113 , ASP A:117 , HOH A:2328 , ALA B:150 , ARG B:151 , SER B:154 , HOH B:2214BINDING SITE FOR RESIDUE GOL A1281
2AC2SOFTWARETYR A:71 , ALA A:72 , TRP A:73 , ALA A:74 , PRO A:124 , SER A:126 , HOH A:2330BINDING SITE FOR RESIDUE GOL A1282
3AC3SOFTWARETYR A:66 , ASN A:67 , VAL A:70 , TYR A:71 , PRO A:128 , HOH A:2331 , HOH A:2332BINDING SITE FOR RESIDUE GOL A1283
4AC4SOFTWAREGLN A:230 , HOH A:2334 , HOH A:2335BINDING SITE FOR RESIDUE GOL A1284
5AC5SOFTWAREHIS A:114 , ALA A:150 , ARG A:151 , SER A:154 , HIS B:114 , ASP B:117 , HOH B:2268BINDING SITE FOR RESIDUE GOL B1281
6AC6SOFTWAREPRO B:253 , ARG B:254 , HOH B:2269 , DG E:292BINDING SITE FOR RESIDUE GOL B1282
7AC7SOFTWARETYR B:66 , ASN B:67 , VAL B:70 , TYR B:71 , PRO B:128 , GLU B:129 , HOH B:2096BINDING SITE FOR RESIDUE IPA B1283

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OE4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OE4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OE4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OE4)

(-) Exons   (0, 0)

(no "Exon" information available for 1OE4)

(-) 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: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 d1oe4a_ A: Single-strand selective monofunctional uracil-DNA glycosylase SMUG1                                                                                                                                                                        SCOP domains
               CATH domains 1oe4A00 A:36-280 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......hhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oe4 A  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 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 d1oe4b_ B: Single-strand selective monofunctional uracil-DNA glycosylase SMUG1                                                                                                                                                                        SCOP domains
               CATH domains 1oe4B00 B:36-280 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                                    CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------UDG-1oe4B01 B:127-271                                                                                                                            --------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------UDG-1oe4B02 B:127-271                                                                                                                            --------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------UDG-1oe4B03 B:127-271                                                                                                                            --------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------UDG-1oe4B04 B:127-271                                                                                                                            --------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.........eeehhhhhhhhhhhhhhhhhh.....eeeee......hhhhhh....hhhhhhhh...................hhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eeeee....eee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oe4 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
                                            
                 1oe4 E 281 CCCGTGAGTCCG 292
                                   290  


Chain F from PDB  Type:DNA  Length:12
                                            
                 1oe4 F 293 CGGACTxACGGG 304
                                  |302  
                                299-3DR
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: UDG] (24)
(-)
Family: UDG (24)
(-)
Xenopus laevis (African clawed frog) (1)
1aUDG-1oe4B01B:127-271
1bUDG-1oe4B02B:127-271
1cUDG-1oe4B03B:127-271
1dUDG-1oe4B04B:127-271

(-) 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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  1oe4
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  SMUG1_XENLA | Q9YGN6
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 Related Entries

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

UniProtKB/Swiss-Prot
        SMUG1_XENLA | Q9YGN6: 1oe5 1oe6

(-) Related Entries Specified in the PDB File

1oe5 XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE
1oe6 XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE