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(-) Description

Title :  STRUCTURAL BASIS FOR A NEW TEMPLATED ACTIVITY BY TERMINAL DEOXYNUCLEOTIDYL TRANSFERASE: IMPLICATIONS FOR V(D)J RECOMBINATION
 
Authors :  J. Loc'H, S. Rosario, M. Delarue
Date :  07 Aug 15  (Deposition) - 27 Jul 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Tdt, Synapsis, Double Strand Breaks, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Loc'H, S. Rosario, M. Delarue
Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination.
Structure V. 24 1452 2016
PubMed-ID: 27499438  |  Reference-DOI: 10.1016/J.STR.2016.06.014

(-) Compounds

Molecule 1 - TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DNTT
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*TP*TP*TP*TP*GP*GP*C)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*AP*AP*AP*AP*A)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2MG1Ligand/IonMAGNESIUM ION
3NA1Ligand/IonSODIUM ION
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:343 , ASP A:345 , SO4 A:603 , HOH A:720 , HOH A:852 , DC C:8binding site for residue MG A 601
2AC2SOFTWARETHR A:253 , VAL A:255 , VAL A:258 , HOH A:1003 , DG C:6 , HOH C:104binding site for residue NA A 602
3AC3SOFTWAREGLY A:332 , GLY A:333 , ARG A:336 , ASP A:345 , MG A:601 , HOH A:756 , HOH A:777 , HOH A:852 , HOH A:944 , DC C:8 , HOH C:107binding site for residue SO4 A 603
4AC4SOFTWAREGLY A:425 , LYS A:426binding site for residue SO4 A 604
5AC5SOFTWAREASN A:184 , GLY A:186 , SER A:187 , HOH A:848binding site for residue ACT A 605
6AC6SOFTWARELYS A:338 , MET A:339 , THR A:340 , HOH A:796binding site for residue ACT A 606
7AC7SOFTWAREGLY A:213 , LYS A:222binding site for residue ACT A 607
8AC8SOFTWAREPRO A:324 , ASP A:325 , GLU A:352 , HOH A:770binding site for residue PG4 A 608

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D49)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:390 -Pro A:391
2Gly A:452 -Ser A:453

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D49)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D49)

(-) Exons   (0, 0)

(no "Exon" information available for 5D49)

(-) 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:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               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...eeeeehhhhh...ee..eeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhh...........eeeeeeeeee.hhh.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee....ee....hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d49 A 148 KKISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPSRKVDALDHFQKCFLILKLDHGRVHEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA 510
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       424       434       444       454       464       474       484       494       504      
                                                                                                                                                                                                                                                                                                      416|                                                                                      
                                                                                                                                                                                                                                                                                                       424                                                                                      


Chain B from PDB  Type:DNA  Length:6
                                      
                 5d49 B   1 AAAAAC   6


Chain C from PDB  Type:DNA  Length:8
                                        
                 5d49 C   1 TTTTTGGC   8


Chain D from PDB  Type:DNA  Length:8
                                        
                 5d49 D   1 TTTTTGGC   8


Chain E from PDB  Type:DNA  Length:5
                                     
                 5d49 E   1 AAAAA   5
   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 5D49)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D49)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D49)

(-) Gene Ontology  (13, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:390 - Pro A:391   [ RasMol ]  
    Gly A:452 - Ser A:453   [ RasMol ]  
 

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  5d49
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q3UZ80_MOUSE | Q3UZ80: 5d46 5d4b
        TDT_MOUSE | P09838: 1jms 1kdh 1kej 4i27 4i28 4i29 4i2a 4i2b 4i2c 4i2d 4i2e 4i2f 4i2g 4i2h 4i2i 4i2j 4iqt 4iqu 4iqv 4iqw 4qz8 4qz9 4qza 4qzb 4qzc 4qzd 4qze 4qzf 4qzg 4qzh 4qzi 5d46 5d4b

(-) Related Entries Specified in the PDB File

5d46