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(-) Description

Title :  BINARY COMPLEX OF MURINE TERMINAL DEOXYNUCLEOTIDYL TRANSFERASE WITH A PRIMER SINGLE STRANDED DNA
 
Authors :  M. Delarue, J. B. Boule, J. Lescar, N. Expert-Bezancon, N. Jourdan, N. Sukumar, F. Rougeon, C. Papanicolaou
Date :  13 Nov 01  (Deposition) - 13 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Polymerase, Nucleotidyl Transferase, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Delarue, J. B. Boule, J. Lescar, N. Expert-Bezancon, N. Jourdan, N. Sukumar, F. Rougeon, C. Papanicolaou
Crystal Structures Of A Template-Independent Dna Polymerase: Murine Terminal Deoxynucleotidyltransferase.
Embo J. V. 21 427 2002
PubMed-ID: 11823435  |  Reference-DOI: 10.1093/EMBOJ/21.3.427
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(P*(BRU)P*(BRU)P*(BRU)P*(BRU))-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE SHORT ISOFORM
    Chains: A
    EC Number: 2.7.7.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1BRU4Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3NA1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:343 , ASP A:345 , ASP A:434 , TRP A:450 , BRU D:3 , BRU D:4BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWARETHR A:253 , VAL A:255 , VAL A:258 , BRU D:2BINDING SITE FOR RESIDUE NA A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KDH)

(-) 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 1KDH)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_XPS00522 DNA polymerase family X signature.TDT_MOUSE332-351  1A:332-351

(-) Exons   (0, 0)

(no "Exon" information available for 1KDH)

(-) 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
 aligned with TDT_MOUSE | P09838 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:383
                                   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       417       427       437       447       457       467       477       487       497       507       517       527   
            TDT_MOUSE   148 KKISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPSRKVDALDHFQKCFLILKLDHGRVHSEKSGQQEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHALYDRTKGKTVTISPLDGKVSKLQKALRVFLEAESEEEIFAHLGLDYIEPWERNA 530
               SCOP domains d1kdha1 A:148-242 Terminal deoxynucleotidyl transferase                                        d1kdha3 A:243-302 Terminal deoxynucleotidyl transferase     d1kdha4 A:303-510 Terminal deoxynucleotidyl transferase                                                                                                                                                                              SCOP domains
               CATH domains 1kdhA01 A:148-242  [code=1.10.150.110, no name defined]                                        1kdhA02 A:243-301                                          1kdhA03 A:302-440 Beta Polymerase, domain 2                                                                                                1kdhA04 A:441-509 Beta Polymerase, domain                     3                          - CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------DNA_pol_lambd_f-1kdhA02 A:249-301                    -----------NTP_transf_2-1kdhA01 A:313-404                                                              ----------------   -----------------------------------------------------------                    ---------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhh...eeeee..............----.....eeeeeeeee.hhh.....---....eeeeeeeeeeee..hhhhhhhhhh.hhhhhhhhhhhhhhhhheee....eee...--------------------.eee...hhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kdh A 148 KKISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPSR----LDHFQKCFLILKLDHGRVHSEKS---EGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHALYDRTK--------------------RVFLEAESEEEIFAHLGLDYIEPWERNA 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     |   -|      407       417  |   |427       437       447       457       467       477    |    -         -     | 487       497       507   
                                                                                                                                                                                                                                                                               393  398                   420 424                                                       482                  483                           


Chain D from PDB  Type:DNA  Length:4
                                    
                 1kdh D   1 uuuu   4
                            ||||
                            1-BRU
                             2-BRU
                              3-BRU
                               4-BRU
   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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: NTP_transf (45)
(-)
Clan: no clan defined [family: DNA_pol_lambd_f] (69)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TDT_MOUSE | P09838)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003912    DNA nucleotidylexotransferase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:0034061    DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    GO:0006304    DNA modification    The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TDT_MOUSE | P09838: 1jms 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 5d4b

(-) Related Entries Specified in the PDB File

1bpy TERNARY COMPLEX OF HUMAN POLYMERASE BETA
1jms UNLIGANDED MURINE TERMINAL DEOXYNUCLEOTIDYL TRANSFERASE
1kej TDT COMPLEXED WITH DDATP