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(-) Description

Title :  TERNARY COMPLEX OF MOUSE TDT WITH SSDNA AND AMPCPP
 
Authors :  J. Gouge, M. Delarue
Date :  21 Nov 12  (Deposition) - 24 Jul 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Terminal Transferase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Gouge, S. Rosario, F. Romain, P. Beguin, M. Delarue
Structures Of Intermediates Along The Catalytic Cycle Of Terminal Deoxynucleotidyltransferase: Dynamical Aspects Of The Two-Metal Ion Mechanism.
J. Mol. Biol. V. 425 4334 2013
PubMed-ID: 23856622  |  Reference-DOI: 10.1016/J.JMB.2013.07.009

(-) 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*A)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MN2Ligand/IonMANGANESE (II) ION
3NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:253 , VAL A:255 , VAL A:258 , HOH A:922 , DA C:4 , HOH C:101BINDING SITE FOR RESIDUE NA A 601
2AC2SOFTWAREGLY A:332 , GLY A:333 , ARG A:336 , GLY A:341 , HIS A:342 , ASP A:343 , ASP A:345 , PHE A:405 , ASP A:434 , GLY A:449 , TRP A:450 , GLY A:452 , MN A:603 , MN A:604 , HOH A:859 , HOH A:874 , HOH A:884 , HOH A:962 , HOH A:981 , HOH A:991 , DA C:4BINDING SITE FOR RESIDUE APC A 602
3AC3SOFTWAREASP A:343 , ASP A:345 , ASP A:434 , APC A:602 , MN A:604 , HOH A:962BINDING SITE FOR RESIDUE MN A 603
4AC4SOFTWAREASP A:343 , ASP A:345 , APC A:602 , MN A:603 , HOH A:981BINDING SITE FOR RESIDUE MN A 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I2C)

(-) 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 4I2C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I2C)

(-) Exons   (0, 0)

(no "Exon" information available for 4I2C)

(-) 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:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4i2ca1 A:149-242 automated matches                                                           d4i2ca2 A:243-302 automated matches                         d4i2ca3 A:303-510 automated matches                                                                                                                                                                           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....................eeeeeeeeee.hhh.........eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee....ee....hhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i2c A 149 KISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPSRKVDALDHFQKCFLILKLDHGRVHSEKQEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA 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       398       408       418||     431       441       451       461       471       481       491       501         
                                                                                                                                                                                                                                                                                                        419|                                                                                       
                                                                                                                                                                                                                                                                                                         423                                                                                       


Chain C from PDB  Type:DNA  Length:3
                                   
                 4i2c C   2 AAA   4
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I2C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I2C)

(-) 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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  4i2c
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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 4i2d 4i2e 4i2f 4i2g 4i2h 4i2i 4i2j 4iqt 4iqu 4iqv 4iqw 4qz8 4qz9 4qza 4qzb 4qzc 4qzd 4qze 4qzf 4qzg 4qzh 4qzi 5d46 5d49 5d4b

(-) Related Entries Specified in the PDB File

4i27 4i28 4i29 4i2a 4i2b 4i2d 4i2e 4i2f 4i2g 4i2h 4i2i 4i2j