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(-) Description

Authors :  C. Oefner, D. H. Gelfand, S. Stoffel, F. K. Winkler
Date :  09 Oct 96  (Deposition) - 12 Mar 97  (Release) - 24 Feb 09  (Revision)
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Nucleotidyltransferase, Dna-Directed Dna Polymerase, Dna Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  

PubMed: search
(for further references see the PDB file header)

(-) Compounds

    Cell Line293
    EC Number2.7.7.7
    Expression SystemESCHERICHIA COLI
    Expression System Strain293
    Expression System Taxid562
    FragmentSTOFFEL FRAGMENT, RESIDUES 290 - 832
    Organism ScientificTHERMUS AQUATICUS
    Organism Taxid271

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1JXE)

(-) Sites  (0, 0)

(no "Site" information available for 1JXE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
1Trp A:299 -Pro A:300
2Asp A:578 -Pro A:579

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JXE)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1DNA_POLYMERASE_APS00447 DNA polymerase family A signature.DPO1_THEAQ659-678  1A:659-678

(-) Exons   (0, 0)

(no "Exon" information available for 1JXE)

(-) 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:525
 aligned with DPO1_THEAQ | P19821 from UniProtKB/Swiss-Prot  Length:832

    Alignment length:540
                                   302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832
               SCOP domains d1jxea1 A:293-422 Exonuclease domain of prokaryotic DNA polymerase                                                                d1jxea2 A:423-832 DNA polymerase I (Klenow fragment)                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1jxeA01 A:293-446  [code=3.30.420.10, no name defined]                                                                                                    1jxeA02 A:447-563 Taq DNA Polymerase; Chain T, domain                4                                               1jxeA03 A:564-613,A:758-830                       1jxeA04 A:614-757 5' to 3' exonuclease, C-terminal subdomain                                                                                    1jxeA03 A:564-613,A:758-830  [code=, no name defined]         -- CATH domains
               Pfam domains Taq-exonuc-1jxeA02 A:293-420                                                                                                    ------------------------------DNA_pol_A-1jxeA01 A:451-830                                                                                                                                                                                                                                                                                                                                                                 -- Pfam domains
         Sec.struct. author ..eee........eeeeee.........eeeeeeee..eeee...hhhhhhh........hhhhhhhhhhh.........hhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh...---------------.hhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhh..........eee.........eee...hhh.....hhhhhhhhh......eeeeeeee..hhhhhhhhhh..hhhhhhhh....hhhhhhhhhh...hhh..hhhhhhhhhhhhhhh.....hhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.eee.....eee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeee...hhhhhhhhhhhhh..........eeeeee..hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_A    ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                                   302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       | -         -   |   522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832
                                                                                                                                                                                                                                         500             516                                                                                                                                                                                                                                                                                                                            

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (4, 4)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPO1_THEAQ | P19821)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0001882    nucleoside binding    Interacting selectively and non-covalently with a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose.
    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:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.


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    Asp A:578 - Pro A:579   [ RasMol ]  
    Trp A:299 - Pro A:300   [ RasMol ]  

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 Related Entries

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

        DPO1_THEAQ | P198211bgx 1ktq 1qss 1qsy 1qtm 1taq 1tau 2ktq 3ktq 3lwl 3lwm 3m8r 3m8s 3ojs 3oju 3po4 3po5 3py8 3rr7 3rr8 3rrg 3rrh 3rtv 3sv3 3sv4 3syz 3sz2 3t3f 4bwj 4bwm 4c8k 4c8l 4c8m 4c8n 4c8o 4cch 4df4 4df8 4dfj 4dfk 4dfm 4dfp 4dle 4dlg 4elt 4elu 4elv 4ktq 4n56 4n5s 4xiu 5e41 5ktq 5nkl 5szt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1JXE)