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(-) Description

Title :  ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE COMPLEX WITH URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN
 
Authors :  K. Saikrishnan, M. B. Sagar, R. Ravishankar, S. Roy, K. Purnapatre, P. Handa, U. Varshney, M. Vijayan
Date :  10 May 02  (Deposition) - 10 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Glycosylase, Inhibitor, Dna Repair, Base Excision, Complex (Hydrolase/Inhibitor), Hydrolase/Hydrolase Inhibitor Complex (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
    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
 
Molecule 2 - URACIL-DNA GLYCOSYLASE INHIBITOR
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS PHAGE PBS2
    Organism Taxid: 10684

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1LQG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala C:62 -Pro C:63
2Ala D:62 -Pro D:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1LQG)

(-) 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: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 d1lqga_ A: Uracil-DNA glycosylase                                                                                                                                                                                                  SCOP domains
               CATH domains 1lqgA00 A:3-228 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee................hhhhhhhhhhhhhhhhh...eeeeehhhhh...........eeeee...hhhhhh......hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------U_DNA_GLYC------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lqg A   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      


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with UNG_ECOLI | P12295 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:224
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    
            UNG_ECOLI     2 ANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLP 225
               SCOP domains d1lqgb_ B: Uracil-DNA glycosylase                                                                                                                                                                                                SCOP domains
               CATH domains 1lqgB00 B:2-225 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                CATH domains
           Pfam domains (1) ------------------------------------------------UDG-1lqgB01 B:50-211                                                                                                                                              -------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------UDG-1lqgB02 B:50-211                                                                                                                                              -------------- Pfam domains (2)
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee................hhhhhhhhhhhhhhhhh...eeeeehhhhh...........eeeee...............hhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------U_DNA_GLYC--------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lqg B   2 ANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLP 225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    


Chain C from PDB  Type:PROTEIN  Length:73
 aligned with UNGI_BPPB2 | P14739 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:73
                                    21        31        41        51        61        71        81   
           UNGI_BPPB2    12 TGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
               SCOP domains d1lqgc_ C: Uracil-DNA glycosylase inhibitor protein                       SCOP domains
               CATH domains 1lqgC00 C:12-84  [code=3.10.450.20, no name defined]                      CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeehhhhhhhhhh......eeeeee.......eeeeeee......eeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 1lqg C  12 TGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
                                    21        31        41        51        61        71        81   


Chain D from PDB  Type:PROTEIN  Length:70
 aligned with UNGI_BPPB2 | P14739 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:70
                                    24        34        44        54        64        74        84
           UNGI_BPPB2    15 QLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
               SCOP domains d1lqgd_ D: Uracil-DNA glycosylase inhibitor protein                    SCOP domains
               CATH domains 1lqgD00 D:15-84  [code=3.10.450.20, no name defined]                   CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeehhhhhhhhhh......eeeeeeee....eeeeeeee......eeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 1lqg D  15 QLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
                                    24        34        44        54        64        74        84
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (10, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

Chain C,D   (UNGI_BPPB2 | P14739)
molecular function
    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).

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  1lqg
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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
        UNGI_BPPB2 | P14739: 1eui 1lqm 1udi 1ugh 1ugi 1uug 2j8x 2ugi 2uug 2zhx 4lyl
        UNG_ECOLI | P12295: 1eug 1eui 1flz 1lqj 1lqm 1uug 2eug 2uug 3eug 3uf7 4eug 5eug

(-) Related Entries Specified in the PDB File

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