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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  NON-PRODUCTIVE MUG-DNA COMPLEX
 
Authors :  T. E. Barrett, R. Savva, T. Barlow, T. Brown, J. Jiricny, L. H. Pearl
Date :  21 Sep 02  (Deposition) - 27 Sep 02  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Glycosylase, Cis-Platin, Inter-Strand, Non-Productive, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Barrett, R. Savva, T. Barlow, T. Brown, J. Jiricny, L. H. Pearl
Structure Of A Dna Base-Excision Product Resembling A Cisplatin Inter-Strand Adduct.
Nat. Struct. Biol. V. 5 697 1998
PubMed-ID: 9699633  |  Reference-DOI: 10.1038/1394

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*CP*GP*AP*GP*(AAB)P*TP*CP*GP*CP*G)-3'
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - G/U MISMATCH-SPECIFIC DNA GLYCOSYLASE
    Chains: A, B
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PTRC99A
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MUG
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: MUG DNA GLYCOSYLASE, MISMATCH-SPECIFIC URACIL DNA- GLYCOSYLASE, UDG

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1AAB2Mod. Nucleotide2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1MTL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MTL)

(-) 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:157
 aligned with MUG_ECOLI | P0A9H1 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   
            MUG_ECOLI     2 VEDILAPGLRVVFCGINPGLSSAGTGFPFAHPANRFWKVIYQAGFTDRQLKPQEAQHLLDYRCGVTKLVDRPTVQANEVSKQELHAGGRKLIEKIEDYQPQALAILGKQAYEQGFSQRGAQWGKQTLTIGSTQIWVLPNPSGLSRVSLEKLVEAYRELDQALV 164
               SCOP domains d1mtla_ A: G:T/U mismatch-specific DNA glycosylase, Mug                                                                                                             SCOP domains
               CATH domains 1mtlA00 A:2-164 Uracil-DNA Glycosylase, subunit E                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee...................hhhhhhhhh.......hhhhhhhhhhh.eeeee..------....hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhh.......eeeeeee..eeeee..........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mtl A   2 VEDILAPGLRVVFCGINPGLSSAGTGFPFAHPANRFWKVIYQAGFTDRQLKPQEAQHLLDYRCGVTKLV------ANEVSKQELHAGGRKLIEKIEDYQPQALAILGKQAYEQGFSQRGAQWGKQTLTIGSTQIWVLPNPSGLSRVSLEKLVEAYRELDQALV 164
                                    11        21        31        41        51        61        |-     |  81        91       101       111       121       131       141       151       161   
                                                                                               70     77                                                                                       


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with MUG_ECOLI | P0A9H1 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
            MUG_ECOLI     1 MVEDILAPGLRVVFCGINPGLSSAGTGFPFAHPANRFWKVIYQAGFTDRQLKPQEAQHLLDYRCGVTKLVDRPTVQANEVSKQELHAGGRKLIEKIEDYQPQALAILGKQAYEQGFSQRGAQWGKQTLTIGSTQIWVLPNPSGLSRVSLEKLVEAYRELDQALV 164
               SCOP domains d1mtlb_ B: G:T/U mismatch-specific DNA glycosylase, Mug                                                                                                              SCOP domains
               CATH domains 1mtlB00 B:1-164 Uracil-DNA Glycosylase, subunit E                                                                                                                    CATH domains
           Pfam domains (1) --UDG-1mtlB01 B:3-163                                                                                                                                              - Pfam domains (1)
           Pfam domains (2) --UDG-1mtlB02 B:3-163                                                                                                                                              - Pfam domains (2)
         Sec.struct. author ...........eeeee...................hhhhhhhhh.......hhhhhhhhhhh.eeeee.....----...hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhh.......eeeeeee..eeeee..........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mtl B   1 MVEDILAPGLRVVFCGINPGLSSAGTGFPFAHPANRFWKVIYQAGFTDRQLKPQEAQHLLDYRCGVTKLVDRP----NEVSKQELHAGGRKLIEKIEDYQPQALAILGKQAYEQGFSQRGAQWGKQTLTIGSTQIWVLPNPSGLSRVSLEKLVEAYRELDQALV 164
                                    10        20        30        40        50        60        70  |    |80        90       100       110       120       130       140       150       160    
                                                                                                   73   78                                                                                      


Chain C from PDB  Type:DNA  Length:12
                                            
                 1mtl C 201 CGCGAGxTCGCG 212
                                  |210  
                                207-AAB 


Chain D from PDB  Type:DNA  Length:12
                                            
                 1mtl D 213 CGCGAGxTCGCG 224
                                  |222  
                                219-AAB
   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, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: UDG] (24)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MUG_ECOLI | P0A9H1)
molecular function
    GO:0019104    DNA N-glycosylase activity    Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
    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.
    GO:0008263    pyrimidine-specific mismatch base pair DNA N-glycosylase activity    Catalysis of the removal of mismatched pyrimidine bases in DNA. Enzymes with this activity recognize and remove pyrimidines present in mismatches by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apyrimidinic (AP) site.
    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:0006285    base-excision repair, AP site formation    The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MUG_ECOLI | P0A9H1: 1mug 1mwi 1mwj

(-) Related Entries Specified in the PDB File

1mug 1MUG IS THE NATIVE MUG STRUCTURE