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(-) Description

Title :  CRYSTAL STRUCTURE DETERMINATION OF URACIL-DNA N-GLYCOSYLASE (UNG) FROM DEINOCOCCUS RADIODURANS IN COMPLEX WITH DNA - NEW INSIGHTS INTO THE ROLE OF THE LEUCINE-LOOP FOR DAMAGE RECOGNITION AND REPAIR
 
Authors :  H. L. Pedersen, K. A. Johnson, C. E. Mcvey, I. Leiros, E. Moe
Date :  24 Jun 14  (Deposition) - 12 Aug 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydrolase-Dna Complex, Base Excision Repair, Radiation Resistance, Dna Damage, Dna Repair, Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Pedersen, K. A. Johnson, I. Leiros, E. Moe
Crystal Structure Determination Of Uracil-Dna N- Glycosylase (Ung) From Deinococcus Radiodurans In Complex With Dna - New Insights Into The Role Of The Leucine-Loop For Damage Recognition And Repair
Acta Crystallogr. , Sect. D V. 71 2137 2015
PubMed: search  |  Reference-DOI:

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Other Details: RESIDUES 1-15 AND 246-247 NOT VISIBLE IN ELECTRON DENSITY
    Synonym: UDG, URACIL DNA GLYCOSYLASE
 
Molecule 2 - 5'-D(*CP*CP*TP*AP*TP*CP*CP*AP*AAB*GP*TP*CP*TP*CP*CP*G)-3'
    Chains: B
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: NUCLEOTIDE 9 IS ABASIC
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*CP*GP*GP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*AP*G)-3'
    Chains: C
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1AAB1Mod. Nucleotide2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:84 , TYR A:85 , SER A:95 , PHE A:96 , ASN A:142BINDING SITE FOR RESIDUE CL A1245
2AC2SOFTWAREGLN A:82 , ALA A:152 , HOH A:2199 , AAB B:9 , DG B:10BINDING SITE FOR RESIDUE GOL A1246

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UQM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:57 -Pro A:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UQM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UQM)

(-) Exons   (0, 0)

(no "Exon" information available for 4UQM)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee....ee..........hhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhh.....eeeee...hhhhhhhh...hhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uqm A  16 RPIIPANLPEDWQEALLPEFSAPYFHELTDFLRQERKEYTIYPPAPDVFNALRYTPLGEVKVLILGQDPYHGPNQAHGLSFSVRPGVRVPPSLRNIYKELTEDIPGFVAPKHGYLRSWAEQGVLLLNAVLTVRAAQANSHQGKGWEHFTDAVIKAVNAKEERVVFILWGSYARKKKKLITGKNHVVIESGHPSPLSEQYFFGTRPFSKTNEALEKAGRGPVEWQLPATV 244
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235         


Chain B from PDB  Type:DNA  Length:12
                                            
                 4uqm B   4 ATCCAxGTCTCC  15
                                 |  13  
                                 9-AAB  


Chain C from PDB  Type:DNA  Length:11
                                           
                 4uqm C   3 GGAGACATGGA  13
                                    12
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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  (0, 0)

(no "SCOP Domain" information available for 4UQM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UQM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UQM)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Tyr A:57 - Pro A:58   [ RasMol ]  
 

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 Related Entries

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        UNG_DEIRA | Q9RWH9: 2boo 3ufm

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