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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH TRAPPED 4'-METHYLATED DTTP
 
Authors :  K. Diederichs, A. Marx, K. Betz
Date :  19 Mar 10  (Deposition) - 07 Jul 10  (Release) - 08 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna, Dna Polymerase, Dna Replication, Nucleotides, Modified Nucleotide, Artificial Nucleotide, Nucleotide Probes, Dna-Binding, Dna-Directed Dna Polymerase, Nucleotidyltransferase, Transferase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Betz, F. Streckenbach, A. Schnur, T. Exner, W. Welte, K. Diederichs A. Marx
Structures Of Dna Polymerases Caught Processing Size-Augmented Nucleotide Probes.
Angew. Chem. Int. Ed. Engl. V. 49 5181 2010
PubMed-ID: 20572212  |  Reference-DOI: 10.1002/ANIE.200905724

(-) Compounds

Molecule 1 - DNA POLYMERASE I, THERMOSTABLE
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21B
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: KLENOW FRAGMENT
    Gene: POLA, POL1
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: TAQ POLYMERASE 1
 
Molecule 2 - DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- 3')
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 13)

Asymmetric/Biological Unit (7, 13)
No.NameCountTypeFull Name
115P1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2ACT4Ligand/IonACETATE ION
3DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4GOL3Ligand/IonGLYCEROL
5HXB1Ligand/Ion4'-METHYLTHYMIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
6MG2Ligand/IonMAGNESIUM ION
7PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMG A:1 , MG A:2 , HOH A:36 , HOH A:68 , HOH A:77 , HOH A:111 , ARG A:573 , ASP A:610 , TYR A:611 , SER A:612 , GLN A:613 , ILE A:614 , GLU A:615 , HIS A:639 , ARG A:659 , LYS A:663 , THR A:664 , PHE A:667 , ASP A:785 , DOC B:112 , DA C:204 , DG C:205BINDING SITE FOR RESIDUE HXB A 113
02AC2SOFTWAREMG A:2 , HOH A:68 , HXB A:113 , ASP A:610 , ASP A:785 , HOH A:840 , DOC B:112BINDING SITE FOR RESIDUE MG A 1
03AC3SOFTWAREMG A:1 , HXB A:113 , ASP A:610 , TYR A:611 , ASP A:785BINDING SITE FOR RESIDUE MG A 2
04AC4SOFTWAREGLY A:672 , ARG A:746 , DA C:203BINDING SITE FOR RESIDUE GOL A 833
05AC5SOFTWAREARG A:425 , TRP A:428 , LEU A:723 , PHE A:724 , TYR A:811BINDING SITE FOR RESIDUE PEG A 834
06AC6SOFTWARETHR A:544 , PRO A:579 , ASN A:580 , ASN A:583 , HOH C:88 , DC C:209 , DC C:210BINDING SITE FOR RESIDUE 15P A 835
07AC7SOFTWAREARG A:313 , TRP A:318 , LEU A:552BINDING SITE FOR RESIDUE ACT A 836
08AC8SOFTWAREASP A:452 , TYR A:455 , ARG A:596 , ILE A:599BINDING SITE FOR RESIDUE ACT A 837
09AC9SOFTWAREARG A:728 , TYR A:729 , VAL A:730 , ACT C:4BINDING SITE FOR RESIDUE ACT A 3
10BC1SOFTWAREDG B:107 , DG B:108BINDING SITE FOR RESIDUE GOL B 3
11BC2SOFTWAREHOH C:31 , DG C:205 , DG C:206 , DC C:207BINDING SITE FOR RESIDUE GOL C 1
12BC3SOFTWAREACT A:3 , ARG A:728 , DG C:206 , DC C:207BINDING SITE FOR RESIDUE ACT C 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M8S)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
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 3M8S)

(-) 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 3M8S)

(-) 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:539
 aligned with DPO1_THEAQ | P19821 from UniProtKB/Swiss-Prot  Length:832

    Alignment length:539
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823         
           DPO1_THEAQ   294 LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
               SCOP domains d3m8sa1 A:294-422 Exonuclease domain of prokaryotic DNA polymerase                                                               d3m8sa2 A:423-832 DNA polymerase I (Klenow fragment)                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Taq-exonuc-3m8sA02 A:294-420                                                                                                   ------------------------------DNA_pol_A-3m8sA01 A:451-830                                                                                                                                                                                                                                                                                                                                                                 -- Pfam domains
         Sec.struct. author .ee.........eeeeee...hhhhh.eeeeeee...eeee..hhhhhhh........hhhhhhhhhhhh........hhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh..................hhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhh.........eee.........eee..........hhhhhhhhh.ee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee.hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_A    ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m8s A 294 LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823         


Chain B from PDB  Type:DNA  Length:12
                                            
                 3m8s B 101 GACCACGGCGCc 112
                                   110 |
                                     112-DOC


Chain C from PDB  Type:DNA  Length:16
                                                
                 3m8s C 201 AAAAGGCGCCGTGGTC 216
                                   210
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M8S)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
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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  3m8s
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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 1tau 2ktq 3ktq 3lwl 3lwm 3m8r 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

1qtm 3ktq 3m8r