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(-) Description

Title :  MOUSE TDT IN COMPLEX WITH A DSB SUBSTRATE, C-A BASE PAIR
 
Authors :  J. Gouge, M. Delarue
Date :  27 Jul 14  (Deposition) - 10 Jun 15  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,D,T,U
Keywords :  Terminal Deoxynucleotidyltransferase, Nucleus, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Gouge, S. Rosario, F. Romain, F. Poitevin, P. Beguin, M. Delarue
Structural Basis For A Novel Mechanism Of Dna Bridging And Alignment In Eukaryotic Dsb Dna Repair.
Embo J. V. 34 1126 2015
PubMed-ID: 25762590  |  Reference-DOI: 10.15252/EMBJ.201489643

(-) Compounds

Molecule 1 - DNA NUCLEOTIDYLEXOTRANSFERASE
    Chains: A
    EC Number: 2.7.7.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SEE REMARK 999
    Gene: DNTT, TDT
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: TERMINAL ADDITION ENZYME, TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE, TDT, TERMINAL TRANSFERASE
 
Molecule 2 - 5'-D(*AP*AP*AP*AP*AP*C)-3'
    Chains: D, U
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*TP*TP*TP*TP*GP*A)-3'
    Chains: T
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ADTU

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1DCT1Ligand/Ion2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:343 , ASP A:345 , DCT A:604 , HOH A:849BINDING SITE FOR RESIDUE MG A 601
2AC2SOFTWAREASP A:343 , ASP A:345 , ASP A:434 , DCT A:604 , DC U:6BINDING SITE FOR RESIDUE MG A 602
3AC3SOFTWARETHR A:253 , VAL A:255 , VAL A:258 , HOH A:847 , DA U:5 , HOH U:102BINDING SITE FOR RESIDUE NA A 603
4AC4SOFTWAREGLY A:332 , GLY A:333 , ARG A:336 , LYS A:338 , GLY A:341 , HIS A:342 , ASP A:343 , ASP A:345 , GLY A:449 , TRP A:450 , GLY A:452 , ARG A:454 , GLU A:457 , MG A:601 , MG A:602 , HOH A:709 , HOH A:836 , HOH A:849 , HOH A:879 , HOH A:963 , DG T:6 , DC U:6BINDING SITE FOR RESIDUE DCT A 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QZ9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:452 -Ser A:453

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QZ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QZ9)

(-) Exons   (0, 0)

(no "Exon" information available for 4QZ9)

(-) 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...eeeehhhhhh...ee..eeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeee.............eeeeeeeeee.hhh......eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee....eee...hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qz9 A 147 VKKISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKALDHFQKCFLILKLDHGRVHSEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA 510
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386  ||   403       413   ||  429       439       449       459       469       479       489       499       509 
                                                                                                                                                                                                                                                                            389|                 417|                                                                                      
                                                                                                                                                                                                                                                                             397                  424                                                                                      


Chain D from PDB  Type:DNA  Length:6
                                      
                 4qz9 D   1 AAAAAC   6


Chain T from PDB  Type:DNA  Length:7
                                       
                 4qz9 T   1 TTTTTGA   7


Chain U from PDB  Type:DNA  Length:6
                                      
                 4qz9 U   1 AAAAAC   6
   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  (0, 0)

(no "SCOP Domain" information available for 4QZ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QZ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QZ9)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:452 - Ser A:453   [ RasMol ]  
 

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  4qz9
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  TDT_MOUSE | P09838
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  2.7.7.31
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 Related Entries

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

UniProtKB/Swiss-Prot
        TDT_MOUSE | P09838: 1jms 1kdh 1kej 4i27 4i28 4i29 4i2a 4i2b 4i2c 4i2d 4i2e 4i2f 4i2g 4i2h 4i2i 4i2j 4iqt 4iqu 4iqv 4iqw 4qz8 4qza 4qzb 4qzc 4qzd 4qze 4qzf 4qzg 4qzh 4qzi 5d46 5d49 5d4b

(-) Related Entries Specified in the PDB File

1jms 4i27 4qz8 4qza 4qzb 4qzc 4qzd 4qze 4qzf 4qzg 4qzh 4qzi