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(-) Description

Title :  CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  J. Hoseki, A. Okamoto, R. Masui, T. Shibata, Y. Inoue, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Jul 03  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Base Excision Repair, Uracil-Dna Glycosylase, Iron/Sulfer Cluster, Thermophile, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hoseki, A. Okamoto, R. Masui, T. Shibata, Y. Inoue, S. Yokoyama, S. Kuramitsu
Crystal Structure Of A Family 4 Uracil-Dna Glycosylase From Thermus Thermophilus Hb8
J. Mol. Biol. V. 333 515 2003
PubMed-ID: 14556741  |  Reference-DOI: 10.1016/J.JMB.2003.08.030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TTHUDG
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:13 , CYS A:16 , ARG A:22 , LYS A:83 , CYS A:84 , CYS A:100 , TRP A:104BINDING SITE FOR RESIDUE SF4 A 210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UI1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UI1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UI1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UI1)

(-) Exons   (0, 0)

(no "Exon" information available for 1UI1)

(-) 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    
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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:188
 aligned with UDGA_THET8 | Q5SKC5 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        
           UDGA_THET8     2 TLELLQAQAQNCTACRLMEGRTRVVFGEGNPDAKLMIVGEGPGEEEDKTGRPFVGKAGQLLNRILEAAGIPREEVYITNIVKCRPPQNRAPLPDEAKICTDKWLLKQIELIAPQIIVPLGAVAAEFFLGEKVSITKVRGKWYEWHGIKVFPMFHPAYLLRNPSRAPGSPKHLTWLDIQEVKRALDALP 189
               SCOP domains d1ui1a_ A: Thermophilic uracil-DNA glycosylase                                                                                                                                               SCOP domains
               CATH domains 1ui1A00 A:2-189 Uracil-DNA Glycosylase, subunit E                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh......hhh.........ee.....eeeee....hhhhhh......hhhhhhhhhhh.....hhh.eeee......hhh....hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhh.....hhhh....eee..eee.....hhhhhh........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ui1 A   2 TLELLQAQAQNCTACRLmEGRTRVVFGEGNPDAKLmIVGEGPGEEEDKTGRPFVGKAGQLLNRILEAAGIPREEVYITNIVKCRPPQNRAPLPDEAKICTDKWLLKQIELIAPQIIVPLGAVAAEFFLGEKVSITKVRGKWYEWHGIKVFPmFHPAYLLRNPSRAPGSPKHLTWLDIQEVKRALDALP 189
                                    11       |21        31     |  41        51        61        71        81        91       101       111       121       131       141       151 |     161       171       181        
                                            19-MSE            37-MSE                                                                                                             153-MSE
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  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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1UI1)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UDGA_THET8 | Q5SKC5)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UDGA_THET8 | Q5SKC5: 1ui0

(-) Related Entries Specified in the PDB File

1ui0 1UI1 CONTAINS THE WILD-TYPE PROTEIN COMPLEXED WITH URACIL RELATED ID: TTK003000721.1 RELATED DB: TARGETDB