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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO UNCLEAVED SUBSTRATE-CONTAINING DNA
 
Authors :  S. S. Parikh, G. Slupphaug, H. E. Krokan, G. M. Blackburn, J. A. Tainer
Date :  16 Mar 00  (Deposition) - 16 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Alpha/Beta Fold, Uracil-Dna Glycosylase, Protein/Dna, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. S. Parikh, G. Walcher, G. D. Jones, G. Slupphaug, H. E. Krokan, G. M. Blackburn, J. A. Tainer
Uracil-Dna Glycosylase-Dna Substrate And Product Structures: Conformational Strain Promotes Catalytic Efficiency By Coupled Stereoelectronic Effects.
Proc. Natl. Acad. Sci. Usa V. 97 5083 2000
PubMed-ID: 10805771  |  Reference-DOI: 10.1073/PNAS.97.10.5083
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*TP*GP*TP*(P2U)P*AP*TP*CP*TP*T)-3')
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - URACIL-DNA GLYCOSYLASE
    ChainsA
    EC Number3.2.2.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsMITOCHONDRIAL PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1P2U1Mod. Nucleotide2'-DEOXY-PSEUDOURIDINE-5'MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1EMH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:119 -Pro A:120
2Arg A:162 -Pro A:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017094F251SUNG_HUMANDisease (HIGM5)104894380AF242S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_HUMAN147-156  1A:138-147

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002425761ENSE00001130047chr12:109535415-109535616202UNG_HUMAN1-44440--
1.2cENST000002425762cENSE00001130067chr12:109536237-109536443207UNG_HUMAN45-113691A:82-10423
1.3ENST000002425763ENSE00000754701chr12:109536994-10953708996UNG_HUMAN114-145321A:105-13632
1.4ENST000002425764ENSE00000754703chr12:109539707-10953980498UNG_HUMAN146-178331A:137-16933
1.5ENST000002425765ENSE00000754705chr12:109540644-10954073289UNG_HUMAN178-208311A:169-19931
1.6ENST000002425766ENSE00000834681chr12:109541238-109541416179UNG_HUMAN208-267601A:199-25860
1.7ENST000002425767ENSE00001130061chr12:109547634-1095487981165UNG_HUMAN268-313461A:259-30446

(-) 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:223
 aligned with UNG_HUMAN | P13051 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:223
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310   
            UNG_HUMAN    91 PVGFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL 313
               SCOP domains d1emha_ A: Uracil-DNA glycosylase                                                                                                                                                                                               SCOP domains
               CATH domains 1emhA00 A:82-304 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhh..hhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh.....eeeee......hhhhh....hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------S-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------U_DNA_GLYC------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c  PDB: A:82-10Exon 1.3  PDB: A:105-136        Exon 1.4  PDB: A:137-169         -----------------------------Exon 1.6  PDB: A:199-258 UniProt: 208-267                   Exon 1.7  PDB: A:259-304 UniProt: 268-313      Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------Exon 1.5  PDB: A:169-199       --------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1emh A  82 MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL 304
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   

Chain B from PDB  Type:DNA  Length:9
                                         
                 1emh B   2 TGTxATCTT  10
                               |     
                               5-P2U 

Chain C from PDB  Type:DNA  Length:10
                                          
                 1emh C  21 AAAGATAACA  30
                                    30

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UNG_HUMAN | P13051)
molecular function
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0097510    base-excision repair, AP site formation via deaminated base removal    A base-excision repair, AP site formation process occurring via excision of a deaminated base.
    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:0045008    depyrimidination    The disruption of the bond between the sugar in the backbone and the C or T base, causing the base to be removed and leaving a depyrimidinated sugar.
    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.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0045830    positive regulation of isotype switching    Any process that activates or increases the frequency, rate or extent of isotype switching.
    GO:0016446    somatic hypermutation of immunoglobulin genes    Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins.
    GO:0016447    somatic recombination of immunoglobulin gene segments    The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        UNG_HUMAN | P130511akz 1dpu 1emj 1q3f 1ssp 1ugh 1yuo 2hxm 2oxm 2oyt 2ssp 3fcf 3fci 3fck 3fcl 3tkb 4skn 5ayr 5jk7

(-) Related Entries Specified in the PDB File

1akz UDG WITHOUT DNA
1ssp 1SSP CONTAINS THE SAME PROTEIN COMPLEXED TO PRODUCT-CONTAINING DNA
2ssp 2SSP CONTAINS THE L272A MUTANT OF UDG BOUND TO AN ABASIC SITE
4skn 4SKN CONTAINS THE L272R/D145N MUTANT OF UDG BOUND TO PRODUCT DNA