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(-) Description

Title :  MOUSE TDT, F401A MUTANT, IN COMPLEX WITH A DSB SUBSTRATE, C-T 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 :  2.60
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
    ChainsA
    EC Number2.7.7.31
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSEE REMARK 999
    GeneDNTT, TDT
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymTERMINAL ADDITION ENZYME, TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE, TDT, TERMINAL TRANSFERASE
 
Molecule 2 - 5'-D(*AP*AP*AP*AP*AP*C)-3'
    ChainsD, U
    EngineeredYES
    SyntheticYES
 
Molecule 3 - 5'-D(*TP*TP*TP*TP*TP*GP*T)-3'
    ChainsT
    EngineeredYES
    SyntheticYES

 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 , ASP A:434 , DCT A:604 , DC U:6BINDING SITE FOR RESIDUE MG A 601
2AC2SOFTWAREASP A:343 , ASP A:345 , DCT A:604BINDING SITE FOR RESIDUE MG A 602
3AC3SOFTWARETHR A:253 , VAL A:255 , VAL A:258 , DA U:5 , HOH U:101BINDING 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:712 , DG T:6BINDING SITE FOR RESIDUE DCT A 604

(-) SS Bonds  (0, 0)

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

(-) 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 4QZH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QZH)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               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....hhhhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeeeee.hhh.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee....eee...hhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qzh A 149 KISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESQKCFLILKLDHGRVHSGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA 510
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378    || 406       416||     433       443       453       463       473       483       493       503       
                                                                                                                                                                                                                                                                    383|            417|                                                                                     
                                                                                                                                                                                                                                                                     402             425                                                                                     

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

Chain T from PDB  Type:DNA  Length:7
                                       
                 4qzh T   1 TTTTTGT   7

Chain U from PDB  Type:DNA  Length:6
                                      
                 4qzh U   1 AAAAAC   6

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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 4QZH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  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 | 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 4qzi 5d46 5d49 5d4b

(-) Related Entries Specified in the PDB File

1jms 4i27 4qz8 4qz9 4qza 4qzb 4qzc 4qzd 4qze 4qzf 4qzg 4qzi