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(-) Description

Title :  BINARY COMPLEX OF MOUSE TDT WITH AP5A
 
Authors :  J. Gouge, M. Delarue
Date :  21 Nov 12  (Deposition) - 24 Jul 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Terminal Transferase, Transferase (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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1AP51Ligand/IonBIS(ADENOSINE)-5'-PENTAPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3ZN7Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY 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 , ARG A:454 , GLU A:457 , ZN A:602 , MG A:609 , HOH A:730 , HOH A:747 , HOH A:800BINDING SITE FOR RESIDUE AP5 A 601
2AC2SOFTWAREASP A:343 , ASP A:345 , ASP A:434 , AP5 A:601 , MG A:609BINDING SITE FOR RESIDUE ZN A 602
3AC3SOFTWAREHIS A:416 , HOH A:802 , HOH A:803 , HOH A:804BINDING SITE FOR RESIDUE ZN A 603
4AC4SOFTWAREGLU A:307 , HIS A:412 , HOH A:798 , HOH A:863BINDING SITE FOR RESIDUE ZN A 604
5AC5SOFTWAREGLU A:183 , HIS A:466 , HOH A:807BINDING SITE FOR RESIDUE ZN A 605
6AC6SOFTWAREGLU A:264 , HOH A:796BINDING SITE FOR RESIDUE ZN A 606
7AC7SOFTWAREASP A:473 , HIS A:475 , HOH A:775BINDING SITE FOR RESIDUE ZN A 607
8AC8SOFTWAREASP A:179 , CYS A:188 , GLU A:230BINDING SITE FOR RESIDUE ZN A 608
9AC9SOFTWAREASP A:343 , ASP A:345 , AP5 A:601 , ZN A:602 , HOH A:730BINDING SITE FOR RESIDUE MG A 609

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I2I)

(-) 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 4I2I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I2I)

(-) Exons   (0, 0)

(no "Exon" information available for 4I2I)

(-) 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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4i2ia1 A:148-242 automated matches                                                            d4i2ia2 A:243-302 automated matches                         d4i2ia3 A:303-510 automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......hhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhh......hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...eeeehhhhhh...ee..eeeeee....hhhhhhhhhhhhhhhhhhh..eeeee...eeeeeeeeee.hhh......eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee....eee...hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i2i A 148 KKISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDIHFQKCFLILKLDHGRVHSEKKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA 510
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377  ||   406       416  ||   432       442       452       462       472       482       492       502        
                                                                                                                                                                                                                                                                  380|                419|                                                                                    
                                                                                                                                                                                                                                                                   400                 426
   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 4I2I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I2I)

(-) 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 | P09838: 1jms 1kdh 1kej 4i27 4i28 4i29 4i2a 4i2b 4i2c 4i2d 4i2e 4i2f 4i2g 4i2h 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 4i2c 4i2d 4i2e 4i2f 4i2g 4i2h 4i2j