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(-) Description

Title :  EPSTEIN-BARR VIRUS URACIL-DNA GLYCOSYLASE IN COMPLEX WITH UGI FROM PBS-2
 
Authors :  T. Geoui, M. Buisson, N. Tarbouriech, W. P. Burmeister
Date :  31 Oct 06  (Deposition) - 13 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hydrolase-Inhibitor Complex, Hydrolase/Inhibitor Complex, Ebv, Dna Repair, Lytic Protein, Epstein-Barr Virus, Uracil- Dna Glycosylase, Hydrolase, Uracil-Dna Glycosylase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Geoui, M. Buisson, N. Tarbouriech, W. P. Burmeister
New Insights On The Role Of The Gamma-Herpesvirus Uracil-Dna Glycosylase Leucine Loop Revealed By The Structure Of The Epstein-Barr Virus Enzyme In Complex With An Inhibitor Protein.
J. Mol. Biol. V. 366 117 2007
PubMed-ID: 17157317  |  Reference-DOI: 10.1016/J.JMB.2006.11.007

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    ChainsA, C
    EC Number3.2.2.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEXHTB
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentURACIL-DNA GLYCOSYLASE DOMAIN, RESIDUES 25-255
    Organism CommonHHV-4
    Organism ScientificEPSTEIN-BARR VIRUS
    Organism Taxid10376
    StrainB95-8
 
Molecule 2 - URACIL-DNA GLYCOSYLASE INHIBITOR
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSETB
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificBACILLUS PHAGE PBS2
    Organism Taxid10684
    StrainPBS-2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1URE2Ligand/IonUREA
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1URE1Ligand/IonUREA
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1URE1Ligand/IonUREA

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:160 , ALA A:163 , ASP B:61BINDING SITE FOR RESIDUE URE B1085
2AC2SOFTWAREGLY C:160 , ALA C:163 , ASP D:61BINDING SITE FOR RESIDUE URE D1085

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J8X)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:65 -Pro A:66
2Ala B:62 -Pro B:63
3Tyr C:65 -Pro C:66
4Ala D:62 -Pro D:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J8X)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_EBVB984-93
 
  2A:84-93
C:84-93
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_EBVB984-93
 
  1A:84-93
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_EBVB984-93
 
  1-
C:84-93

(-) Exons   (0, 0)

(no "Exon" information available for 2J8X)

(-) 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:230
 aligned with UNG_EBVB9 | P12888 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:230
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255
            UNG_EBVB9    26 ENLLLPDLWLDFLQLSPIFQRKLAAVIACVRRLRTQATVYPEEDMCMAWARFCDPSDIKVVILGQDPYHGGQANGLAFSVAYGFPVPPSLRNIYAELHRSLPEFSPPDHGCLDAWASQGVLLLNTILTVQKGKPGSHADIGWAWFTDHVISLLSERLKACVFMLWGAKAGDKASLINSKKHLVLTSQHPSPLAQNSTRKSAQQKFLGNNHFVLANNFLREKGLGEIDWRL 255
               SCOP domains d2j8xa1 A:26-255 Uracil-DNA glycosylase                                                                                                                                                                                                SCOP domains
               CATH domains 2j8xA00 A:26-255 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...ee......hhhhh..hhhhh.eeeee......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh.....eeeee...hhhhhhh............hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------U_DNA_GLYC------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j8x A  26 ENLLLPDLWLDFLQLSPIFQRKLAAVIACVRRLRTQATVYPEEDMCMAWARFCDPSDIKVVILGQDPYHGGQANGLAFSVAYGFPVPPSLRNIYAELHRSLPEFSPPDHGCLDAWASQGVLLLNTILTVQKGKPGSHADIGWAWFTDHVISLLSERLKACVFMLWGAKAGDKASLINSKKHLVLTSQHPSPLAQNSTRKSAQQKFLGNNHFVLANNFLREKGLGEIDWRL 255
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255

Chain B from PDB  Type:PROTEIN  Length:83
 aligned with UNGI_BPPB2 | P14739 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:83
                                    11        21        31        41        51        61        71        81   
           UNGI_BPPB2     2 TNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
               SCOP domains d2j8xb_ B: Uracil-DNA glycosylase inhibitor protein                                 SCOP domains
               CATH domains 2j8xB00 B:2-84  [code=3.10.450.20, no name defined]                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......eeeeehhhhhhhhhh......eeeeeeee....eeeeeeee......eeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2j8x B   2 TNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
                                    11        21        31        41        51        61        71        81   

Chain C from PDB  Type:PROTEIN  Length:229
 aligned with UNG_EBVB9 | P12888 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:229
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246         
            UNG_EBVB9    27 NLLLPDLWLDFLQLSPIFQRKLAAVIACVRRLRTQATVYPEEDMCMAWARFCDPSDIKVVILGQDPYHGGQANGLAFSVAYGFPVPPSLRNIYAELHRSLPEFSPPDHGCLDAWASQGVLLLNTILTVQKGKPGSHADIGWAWFTDHVISLLSERLKACVFMLWGAKAGDKASLINSKKHLVLTSQHPSPLAQNSTRKSAQQKFLGNNHFVLANNFLREKGLGEIDWRL 255
               SCOP domains d2j8xc_ C: Uracil-DNA glycosylase                                                                                                                                                                                                     SCOP domains
               CATH domains 2j8xC00 C:27-255 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh....ee......hhhhh..hhhhh.eeeee......................hhhhhhhhhhhhhhh..........hhhhhhh.eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh.....eeeee...hhhhhhh............hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------U_DNA_GLYC------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j8x C  27 NLLLPDLWLDFLQLSPIFQRKLAAVIACVRRLRTQATVYPEEDMCMAWARFCDPSDIKVVILGQDPYHGGQANGLAFSVAYGFPVPPSLRNIYAELHRSLPEFSPPDHGCLDAWASQGVLLLNTILTVQKGKPGSHADIGWAWFTDHVISLLSERLKACVFMLWGAKAGDKASLINSKKHLVLTSQHPSPLAQNSTRKSAQQKFLGNNHFVLANNFLREKGLGEIDWRL 255
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246         

Chain D from PDB  Type:PROTEIN  Length:81
 aligned with UNGI_BPPB2 | P14739 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:81
                                    13        23        33        43        53        63        73        83 
           UNGI_BPPB2     4 LSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
               SCOP domains d2j8xd_ D: Uracil-DNA glycosylase inhibitor protein                               SCOP domains
               CATH domains 2j8xD00 D:4-84  [code=3.10.450.20, no name defined]                               CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh......eeeeehhhhhhhhhh......eeeeeeee....eeeeeeee......eeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2j8x D   4 LSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
                                    13        23        33        43        53        63        73        83 

   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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J8X)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (UNG_EBVB9 | P12888)
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: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.

Chain B,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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 Related Entries

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

UniProtKB/Swiss-Prot
        UNGI_BPPB2 | P147391eui 1lqg 1lqm 1udi 1ugh 1ugi 1uug 2ugi 2uug 2zhx 4lyl

(-) Related Entries Specified in the PDB File

1eui ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE COMPLEX WITHURACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN
1lqg ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE COMPLEX WITH URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN
1lqm ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE COMPLEX WITH URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN
1udi
1ugh CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE INCOMPLEX WITH A PROTEIN INHIBITOR : PROTEIN MIMICRY OF DNA
1ugi URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN
1uug ESCHERICHIA COLI URACIL-DEOXYRIBONUCLEIC ACID GLYCOSYLASE:INHIBITOR COMPLEX WITH WILD-TYPE UDG AND WILD-TYPE UGI
2ugi PROTEIN MIMICRY OF DNA FROM CRYSTAL STRUCTURES OF THEURACIL GLYCOSYLASE INHIBITOR PROTEIN AND ITS COMPLEX WITHESCHERICHIA COLI URACIL-DNA GLYCOSYLASE
2uug ESCHERICHIA COLI URACIL-DEOXYRIBONUCLEIC ACID GLYCOSYLASE:INHIBITOR COMPLEX WITH H187D MUTANT UDG AND WILD-TYPE UGI