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(-) Description

Title :  CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  H. Kosaka, N. Nakagawa, R. Masui, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Oct 05  (Deposition) - 17 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Base Excision Repair, Uracil-Dna Glycosylase, Iron/Sulfer Cluster, Thermophile, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kosaka, J. Hoseki, N. Nakagawa, S. Kuramitsu, R. Masui
Crystal Structure Of Family 5 Uracil-Dna Glycosylase Bound To Dna.
J. Mol. Biol. V. 373 839 2007
PubMed-ID: 17870091  |  Reference-DOI: 10.1016/J.JMB.2007.08.022

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TTUDGB
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2DU1Ligand/Ion2'-DEOXYURIDINE-5'-MONOPHOSPHATE
3SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:59 , SER A:65 , PRO A:71 , PHE A:72 , HOH A:230BINDING SITE FOR RESIDUE ACT A 222
2AC2SOFTWAREGLY A:151 , ARG A:152 , HIS A:190 , ASN A:195 , HOH A:228BINDING SITE FOR RESIDUE ACT A 223
3AC3SOFTWARECYS A:13 , LEU A:15 , CYS A:16 , LEU A:19 , PRO A:42 , CYS A:115 , CYS A:130BINDING SITE FOR RESIDUE SF4 A 220
4AC4SOFTWARETRP A:22 , GLU A:25 , PHE A:46 , GLY A:47 , ASP A:48 , LEU A:102 , ARG A:103 , LEU A:104 , HOH A:247 , HOH A:304BINDING SITE FOR RESIDUE DU A 221

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D3Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D3Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2D3Y)

(-) 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:219
 aligned with UDGB_THET8 | Q5SJ65 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           UDGB_THET8     1 MDREAFVQTLTACRLCPRLVAWREEVVGRKRAFRGEPYWARPVPGFGDPEARILLFGLAPGAHGSNRTGRPFTGDASGAFLYPLLHEAGLSSKPESLPGDDLRLYGVYLTAAVRCAPPKNKPTPEELRACARWTEVELGLLPEVRVYVALGRIALEALLAHFGLRKSAHPFRHGAHYPLPGGRHLLASYHVSRQNTQTGRLTREMFLEVLMEAKRLAGL 219
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhh...hhhhh...........ee.....eeeee......hhhhhh.....hhhhhhhhhhhhhh..................eeeee.....hhhhh.hhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhh............eeee...eeeeee...hhhhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d3y A   1 MDREAFVQTLTACRLCPRLVAWREEVVGRKRAFRGEPYWARPVPGFGDPEARILLFGLAPGAHGSNRTGRPFTGDASGAFLYPLLHEAGLSSKPESLPGDDLRLYGVYLTAAVRCAPPKNKPTPEELRACARWTEVELGLLPEVRVYVALGRIALEALLAHFGLRKSAHPFRHGAHYPLPGGRHLLASYHVSRQNTQTGRLTREMFLEVLMEAKRLAGL 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 2D3Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D3Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D3Y)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UDGB_THET8 | Q5SJ65)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UDGB_THET8 | Q5SJ65: 2ddg 2dem 2dp6

(-) Related Entries Specified in the PDB File

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