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(-) Description

Title :  ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE
 
Authors :  K. Saikrishnan, M. B. Sagar, R. Ravishankar, S. Roy, K. Purnapatre, U. Varshney, M. Vijayan
Date :  10 May 02  (Deposition) - 10 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Glycosylase, Dna Repair, Base Excision, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Saikrishnan, M. Bidya Sagar, R. Ravishankar, S. Roy, K. Purnapatre, P. Handa, U. Varshney, M. Vijayan
Domain Closure And Action Of Uracil Dna Glycosylase (Udg): Structures Of New Crystal Forms Containing The Escherichia Coli Enzyme And A Comparative Study Of The Known Structures Involving Udg.
Acta Crystallogr. , Sect. D V. 58 1269 2002
PubMed-ID: 12136137  |  Reference-DOI: 10.1107/S0907444902009599
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A, B, C, D
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: UDG;
URACIL-DNA-GLYCOSYLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LQJ)

(-) Sites  (0, 0)

(no "Site" information available for 1LQJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:38 -Pro A:39
2Tyr B:38 -Pro B:39
3Tyr C:38 -Pro C:39
4Tyr D:38 -Pro D:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_ECOLI57-66
 
 
 		  4A:57-66
B:57-66
C:57-66
D:57-66
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_ECOLI57-66
 
 
 		  1A:57-66
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_ECOLI57-66
 
 
 		  1-
B:57-66
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_ECOLI57-66
 
 
 		  1-
-
C:57-66
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_ECOLI57-66
 
 
 		  1-
-
-
D:57-66

(-) Exons   (0, 0)

(no "Exon" information available for 1LQJ)

(-) 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:228
 aligned with UNG_ECOLI | P12295 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
            UNG_ECOLI     1 MANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAES 228
               SCOP domains d1lqja_ A: Uracil-DNA glycosylase                                                                                                                                                                                                    SCOP domains
               CATH domains 1lqjA00 A:1-228 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh...eeee....ee..........hhhhhhhhhhhhhhhh....eeeeehhhhhhhh........eeeee...............hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------U_DNA_GLYC------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lqj A   1 MANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAES 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with UNG_ECOLI | P12295 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
            UNG_ECOLI     1 MANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPA 226
               SCOP domains d1lqjb_ B: Uracil-DNA glycosylase                                                                                                                                                                                                  SCOP domains
               CATH domains 1lqjB00 B:1-226 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhh.....eeeee...............hhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lqj B   1 MANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPA 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      


Chain C from PDB  Type:PROTEIN  Length:229
 aligned with UNG_ECOLI | P12295 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
            UNG_ECOLI     1 MANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAESE 229
               SCOP domains d1lqjc_ C: Uracil-DNA glycosylase                                                                                                                                                                                                     SCOP domains
               CATH domains 1lqjC00 C:1-229 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhh..............hhhh.eeeee....ee..........hhhhhhhhhhhhhhhh....eeeeehhhhhhhh........eeeee......hhhhh....hhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------U_DNA_GLYC------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lqj C   1 MANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAESE 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         


Chain D from PDB  Type:PROTEIN  Length:226
 aligned with UNG_ECOLI | P12295 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      
            UNG_ECOLI     3 NELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAES 228
               SCOP domains d1lqjd_ D: Uracil-DNA glycosylase                                                                                                                                                                                                  SCOP domains
               CATH domains 1lqjD00 D:3-228 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                  CATH domains
           Pfam domains (1) -----------------------------------------------UDG-1lqjD01 D:50-211                                                                                                                                              ----------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------UDG-1lqjD02 D:50-211                                                                                                                                              ----------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------UDG-1lqjD03 D:50-211                                                                                                                                              ----------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------UDG-1lqjD04 D:50-211                                                                                                                                              ----------------- Pfam domains (4)
         Sec.struct. author ...hhhhhh.hhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhh......eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh...eeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhh.......eeeee...............hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------U_DNA_GLYC------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lqj D   3 NELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAES 228
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: UDG] (24)
(-)
Family: UDG (24)
(-)
Escherichia coli (strain K12) (7)
1aUDG-1lqjD01D:50-211
1bUDG-1lqjD02D:50-211
1cUDG-1lqjD03D:50-211
1dUDG-1lqjD04D:50-211

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (UNG_ECOLI | P12295)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1lqj
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  UNG_ECOLI | P12295
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 Related Entries

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

UniProtKB/Swiss-Prot
        UNG_ECOLI | P12295: 1eug 1eui 1flz 1lqg 1lqm 1uug 2eug 2uug 3eug 3uf7 4eug 5eug

(-) Related Entries Specified in the PDB File

1eui E.COLI UDG-UGI COMPLEX
1lqg
1lqm