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(-) Description

Title :  TAQ POLYMERASE (E.C.2.7.7.7)/DNA/B-OCTYLGLUCOSIDE COMPLEX
 
Authors :  S. H. Eom, J. Wang, T. A. Steitz
Date :  17 Jun 96  (Deposition) - 18 Apr 97  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Protein-Dna Complex, Taq Dna Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Eom, J. Wang, T. A. Steitz
Structure Of Taq Ploymerase With Dna At The Polymerase Active Site.
Nature V. 382 278 1996
PubMed-ID: 8717047  |  Reference-DOI: 10.1038/382278A0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*CP*GP*AP*TP*CP*CP*G)-3')
    Chains: T
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*CP*GP*GP*AP*TP*CP*GP*C)-3')
    Chains: P
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (TAQ POLYMERASE)
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BGL1Ligand/IonB-2-OCTYLGLUCOSIDE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:339 , ARG A:362 , GLU A:363 , HIS A:554 , PRO A:555 , ARG A:556 , TRP A:645 , MET A:646 , GLY A:648 , ALA A:691 , GLU A:694 , ARG A:695BINDING SITE FOR RESIDUE BGL A 1001
2AC2SOFTWAREASP A:18 , HIS A:21 , ASP A:119 , ASP A:142BINDING SITE FOR RESIDUE ZN A 900

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:578 -Pro A:579

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_APS00447 DNA polymerase family A signature.DPO1_THEAQ659-678  1A:659-678

(-) Exons   (0, 0)

(no "Exon" information available for 1TAU)

(-) 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:793
 aligned with DPO1_THEAQ | P19821 from UniProtKB/Swiss-Prot  Length:832

    Alignment length:823
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829   
           DPO1_THEAQ    10 PKGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDAKAPSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLKLSWDLAKVRTDLPLEVDFAKRREPDRERLRAFLERLEFGSLLHEFGLLESPKALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
               SCOP domains d1taua2 A:10-173 5' to 3' exonuclease domain of DNA polymer                ase Taq                                                                                  d1taua1 A:174-289 5' to 3' exonuclease domain of DNA polymerase Taq                                                 d1taua3 A:290-422 Exonuclease domain of prokaryotic DNA polymerase                                                                   d1taua4 A:423-832 DNA polymerase I (Klenow fragment)                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1tauA01 A:10-175 5'-nuclease                                                                                                                                          1tauA02 A:176-248 5' to 3' exonuclease, C-terminal subdomain             ---------------------------------------------------1tauA03 A:300-446  [code=3.30.420.10, no name defined]                                                                                             1tauA04 A:447-561 Taq DNA Polymerase; Chain T, domai              n 4                                              1tauA05 A:562-613,A:758-829                         1tauA06 A:614-757 5' to 3' exonuclease, C-terminal subdomain                                                                                    1tauA05 A:562-613,A:758-829  [code=3.30.70.370, no name defined]        --- CATH domains
               Pfam domains --5_3_exonuc_N-1tauA02 A:12-172                                                                                                                                    -5_3_exonuc-1tauA01 A:174-271                                                                      -------------------Taq-exonuc-1tauA04 A:291-420                                                                                                      ------------------------------DNA_pol_A-1tauA03 A:451-830                                                                                                                                                                                                                                                                                                                                                                 -- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhh.............hhhhhhhhhhhhhhhh...eeeee...----------------.......hhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhh...eeeee...hhhhh.....eeee........hhhhhhh....hhhhhhhhh.......................hhhh..................hhhh....hhhhhhhhh...................hhhhhhhhhh..hhhhhhhhh...................eeeeee....hhh..eeeeeeee..eeee...hhhhhh.........hhhhhhhhhh..........hhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh....--------------....hhhh......hhhhhhhhhhhhhhhhhh...hhhh...........eee.........eee...hhh.....hhhhhhhhh......eeeeeeee..hhhhhhhhhh..hhhhhhhhh...hhhhhhhhhh...hhh..hhhhhhhhhhhhhhhh....hhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhh.eee.....eee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeee..hhhhhhhhhhhhhh..........eeeeee..hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_A    ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tau A  10 PKGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDA----------------RAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLKLSWDLAKVRTDLPLEVDFAKRREPDRERLRAFLERLEFGSLLHEFGLLESPKALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDEL--------------STSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
                                    19        29        39        49        59        |-         -     |  89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489        |-         -   |   519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829   
                                                                                     68               85                                                                                                                                                                                                                                                                                                                                                                                                                          498            513                                                                                                                                                                                                                                                                                                                               


Chain P from PDB  Type:DNA  Length:8
                                        
                 1tau P 958 CGGATCGC 951
                            ||||||||
                          958|||||||
                           957||||||
                            956|||||
                             955||||
                              954|||
                               953||
                                952|
                                 951


Chain T from PDB  Type:DNA  Length:8
                                        
                 1tau T 901 GCGATCCG 908
   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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (5, 6)

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

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: 5_3_exonuc_C (16)
(-)
Clan: PIN (27)
(-)
Clan: no clan defined [family: DNA_pol_A] (69)
(-)
Clan: no clan defined [family: Taq-exonuc] (17)

(-) 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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  1tau
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  DPO1_THEAQ | P19821
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  2.7.7.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO1_THEAQ | P19821: 1bgx 1jxe 1ktq 1qss 1qsy 1qtm 1taq 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

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