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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 :  2.66
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E,F  (1x)
Biol. Unit 2:  B,D,E,F  (1x)
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
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDNTT
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
    ChainsC, D, E
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*TP*TP*TP*TP*TP*GP*G)-3')
    ChainsF
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A C EF
Biological Unit 2 (1x) B DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2NA2Ligand/IonSODIUM ION
3SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:343 , ASP A:345 , DC C:6 , SO4 C:401binding site for residue MG A 601
02AC2SOFTWARETHR A:253 , VAL A:255 , VAL A:258 , DA C:4binding site for residue NA A 602
03AC3SOFTWARELYS A:338 , MET A:339 , THR A:340binding site for residue SO4 A 603
04AC4SOFTWARELYS A:469 , ARG A:480 , SER B:207 , LYS B:209 , GLU B:467 , ARG B:468binding site for residue SO4 A 604
05AC5SOFTWAREASP B:343 , ASP B:345 , SO4 B:603 , HOH B:702 , DC D:6binding site for residue MG B 601
06AC6SOFTWARETHR B:253 , VAL B:255 , VAL B:258 , DA D:4binding site for residue NA B 602
07AC7SOFTWAREGLY B:332 , GLY B:333 , ARG B:336 , ASP B:345 , MG B:601 , HOH B:702 , HOH B:707 , DC D:6binding site for residue SO4 B 603
08AC8SOFTWARELYS B:338 , MET B:339 , THR B:340binding site for residue SO4 B 604
09AC9SOFTWARELYS A:426 , LYS B:426binding site for residue SO4 B 605
10AD1SOFTWAREASN B:184 , GLU B:185 , GLY B:186 , SER B:187 , DA E:1binding site for residue SO4 B 606
11AD2SOFTWAREGLY A:332 , GLY A:333 , ARG A:336 , LYS A:338 , ASP A:345 , MG A:601 , DC C:6 , HOH C:503binding site for residue SO4 C 401
12AD3SOFTWAREDA C:5 , DC C:6 , HOH C:501 , HOH C:502binding site for residue SO4 C 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D4B)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:452 -Ser A:453
2Lys B:426 -Gly B:427
3Gly B:452 -Ser B:453

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D4B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D4B)

(-) Exons   (0, 0)

(no "Exon" information available for 5D4B)

(-) Sequences/Alignments

Asymmetric 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:350
                                                                                                                                                                                                                                                                                                                                                                                              
               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.eeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeee...............eeeeeeeeee.hhh.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee....eee...hhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d4b A 149 KISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKQPSRALDHFQKCFLILKLDHGRVHEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA 510
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       390  ||   403       413  ||   430       440       450       460       470       480       490       500       510
                                                                                                                                                                                                                                                                       386| 393|                416|                                                                                      
                                                                                                                                                                                                                                                                        389  397                 424                                                                                      

Chain B from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...eeeeehhhhh...ee.eeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeee..............eeeeeeeeee.hhh.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eee....eee...hhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d4b B 149 KISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQALDHFQKCFLILKLDHGRVHEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA 510
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388 ||    404       414 ||    431       441       451       461       471       481       491       501         
                                                                                                                                                                                                                                                                           390|                416|                                                                                      
                                                                                                                                                                                                                                                                            397                 424                                                                                      

Chain C from PDB  Type:DNA  Length:6
                                      
                 5d4b C   1 AAAAAC   6

Chain D from PDB  Type:DNA  Length:6
                                      
                 5d4b D   1 AAAAAC   6

Chain E from PDB  Type:DNA  Length:6
                                      
                 5d4b E   1 AAAAAC   6

Chain F from PDB  Type:DNA  Length:7
                                       
                 5d4b F   1 TTTTTGG   7

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    → 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 5D4B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D4B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D4B)

(-) Gene Ontology  (13, 21)

Asymmetric Unit(hide GO term definitions)

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    Gly A:452 - Ser A:453   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q3UZ80_MOUSE | Q3UZ805d46 5d49
        TDT_MOUSE | P098381jms 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 5d49

(-) Related Entries Specified in the PDB File

4d46 4d49