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2.7.7.7: DNA-directed DNA polymerase

This is an abbreviated version!
For detailed information about DNA-directed DNA polymerase, go to the full flat file.

Word Map on EC 2.7.7.7

Reaction

a 2'-deoxyribonucleoside 5'-triphosphate
+
DNAn
=
diphosphate
 +
DNAn+1

Synonyms

3'–5'-exonuclease, ABO4/POL2a/TIL1, Afu polymerase, ASFV DNA polymerase, ASFV Pol X, B-family replicative DNA polymerase, beta type DNA polymerase, Bst DNA polymerase, CpDNApolI, DBH, Dbh DNA polymerase, Dbh polymerase, ddNTP-sensitive DNA polymerase, Deep Vent DNA polymerase, DeepVent DNA polymerase, deoxynucleate polymerase, deoxyribonucleate nucleotidyltransferase, deoxyribonucleic acid duplicase, deoxyribonucleic acid polymerase, deoxyribonucleic duplicase, deoxyribonucleic polymerase, deoxyribonucleic polymerase I, DinB DNA polymerase, DinB homologue, Dmpol zeta, DNA deoxynucleotidyltransferase, DNA duplicase, DNA nucleotidyltransferase, DNA nucleotidyltransferase (DNA-directed), DNA pol, DNA pol B1, DNA Pol eta, DNA Pol lambda, DNA pol NI, DNA pol Y1, DNA polmerase beta, DNA polymerase, DNA polymerase 1, DNA polymerase 2, DNA polymerase 4, DNA polymerase A, DNA polymerase alpha, DNA polymerase B, DNA polymerase B1, DNA polymerase B2, DNA polymerase B3, DNA polymerase beta, DNA polymerase D, DNA polymerase Dbh, DNA polymerase delta, DNA polymerase Dpo4, DNA polymerase epsilon, DNA polymerase eta, DNA polymerase gamma, DNA polymerase I, DNA polymerase II, DNA polymerase III, DNA polymerase III epsilon subunit, DNA polymerase iota, DNA polymerase IV, DNA polymerase kappa, DNA polymerase lambda, DNA polymerase mu, DNA polymerase ny, DNA polymerase pyrococcus kodakaraensis, DNA polymerase theta, DNA polymerase V, DNA polymerase X, DNA polymerase zeta, DNA polymerases B, DNA polymerases D, DNA polymmerase I, DNA primase-polymerase, DNA replicase, DNA replication polymerase, DNA-dependent DNA polymerase, DNAP, DP1Pho, DP2Pho, Dpo1, Dpo2, Dpo3, Dpo4, Dpo4 polymerase, Dpo4-like enzyme, duplicase, error-prone DNA polymerase, error-prone DNA polymerase X, family B-type DNA polymerase, hoPolD, HSV 1 POL, Igni_0062, K4 polymerase, K4pol, K4PolI, kDNA replication protein, KDO XL DNA polymerase, KF(exo-), KF-, Klenow fragment, Klenow-like DNA polymerase I, KOD DNA polymerases, lesion-bypass DNA polymerase, M1 DNA polymerase, M1pol, MacDinB-1, MA_4027, Miranda pol beta protein, mitochondrial DNA polymerase, Mka polB, More, MsDpo4, mtDNA polymerase NI, mtDNA replicase, Neq DNA polymerase, non-replicative DNA polymerase III, nucleotidyltransferase, deoxyribonucleate, OsPOLP1, PabPol D, PabpolB, PabpolD, Pfu, Pfu DNA polymerase, Pfu Pol, Pfu-POl, PH0121, PH0123, phi29 DNA polymerase, phi29 DNApol, PhoPolD, phPol D, Pol, pol alpha, Pol B, Pol B1, pol beta, Pol BI, pol delta, pol E, POl epsilon, Pol eta, Pol gamma, Pol I, Pol II, pol III, pol iota, Pol IV, pol kappa, pol kappaDELTAC, Pol lambda, Pol mu, pol NI, Pol ny, Pol theta, Pol V, pol Vent (exo-), Pol X, Pol zeta, Pol-beta, POL1, Pol2, POL2a, Pol3, Pol31, PolB, POlB1, polbeta, polD, POLD4, Poldelta, POLdelta1, PolDPho, Polepsilon, Poleta, POLG, PolH, polI, POLIB, POLIC, POLID, poliota, Polkappa, PolX, PolY, poly iota, polymerase alpha catalytic subunit A, polymerase III, pORF30, Pwo DNA polymerase, R2 polymerase, R2 reverse transcriptase, R2-RT, RAD30, RB69 DdDp, RB69 DNA Polymerase, RB69pol, Rec1, repair polymerase, replicative DNA polymerase, reverse transcriptase, RKOD DNA polymerase, Rv1537, Rv3056, Saci_0554, sequenase, Sso, Sso DNA pol B1, Sso DNA pol Y1, Sso DNA polymerase Y1, Sso DNApol, Sso pol B1, SSO0552, SSO2448, SsoDpo1, SsoPolB1, SsoPolY, Szi DNA polymerase, T4 DNA polymerase, T7 DNA polymerase, Taq DNA polymerase, Taq Pol I, Taq polymerase, Tba5 DNA polymerase, Tca DNA polymerase, Tga PolB, TGAM_RS07365, Tkod-Pol, translesion DNA polymerase, translesion DNA synthesis polymerase, translesion polymerase Dpo4, UL30/UL42, UmuD'2C, UmuD'2C-RecA-ATP, Vent polymerase, X family DANN polymerase, Y-family DNA polymerase eta

ECTree

     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.7 Nucleotidyltransferases
                2.7.7.7 DNA-directed DNA polymerase

Crystallization

Crystallization on EC 2.7.7.7 - DNA-directed DNA polymerase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 0.1 M sodium acetate, pH 5, 0.2 M NaCl, 16% (w/v) 2-methyl-2,4-pentanedil
-
vapor diffusion at 20°C, crystal structure of is determined at 2.4 A resolution
crystal structure of the catalytic alpha subunit of DNA polymerase III is determined at 2.3 A resolution
-
crystal structure of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and diphosphate, combined equilibrium dialysis and vapor diffusion method
the crystal structure of this fusion protein is solved by a combination of multiwavelength anomalous diffraction and molecular replacement to 3.2 A resolution and shows that RB69 single-stranded DNA binding protein is positioned proximal to the N-terminal domain of RB69 DNA polymerase near the template strand channel
-
T7 DNA polymerase
-
pol beta-DNA complexes dGTP(beta-gamma CF2) and dGTP(beta-gamma CH2) are crystallized by sitting-drop vapor diffusion
sitting drop vapor diffusion, ternary polbeta:DNA:r8-oxo-GTP crystals
hanging drop vapor diffusion, crystal structure at 2.7 A resolution, crystals of HSV POL belong to space group P212121, with typical unit cell dimensions of a = 103.9 A, b = 125.6 A, c = 220.6 A
-
microbatch method, sitting-vapor diffusion method. 2.4 A crystal structure of the polymerase domain of murine Pol l bound to gapped DNA with a correct dNTP at the active site
-
purified native and selenomethionine-labeled MsDpo4, hanging drop vapour diffusion method, 1 mM protein is mmixed with 2.4 M NaCl, and 0.1 M sodium/potassium phosphate, pH 6.4, 72 h, 25°C, optimization of crystallization and cryoprotection method, X-ray diffraction structure determination and analysis at 26 A resolution, molecular replacement
sitting drop vapor diffusion, crystal structures of the POL domain, as apoenzyme and as ternary complex with 3'-dideoxy-terminated DNA primer-template and dNTP
hanging drops method, crystal structure at a resolution of 2.9 A
collection of diffraction data to 3.1 A of the selenomethionine-derivatized crystal, the crystal belongs to the space group C2 with unit cell parameters of a = 93.2 A, b = 124.9 A, c = 87.7 A, alpha = 90°, beta = 109.7°, and gamma = 90°
-
hanging-drop method, structure of the apo form a binary complex of the archael B family DNA polymerase E10 variant with duplex DNA bound in synthesis mode
hanging-drop vapour diffusion method. Crystallization of a stable complex of the DNA polymerase with proliferating cell nuclear antigen (PCNA), using a PCNA monomer mutant. The best ordered crystal diffracts to 3.0 A resolution using synchrotron radiation. The crystals belong to space group P2(1)2(1)2, with unit-cell parameters a = 225.3 A, b = 123.3 A, c = 91.3 A
-
the enzyme is crystallized from 0.08 M ammonium sulfate, 0.05 M Na-cacodylate, pH 6.5, 0.15%(v/v) NP40, 0.05%(v/v) Tween 20 and 4.5%(w/v) polyethylene glycol 6000 by the vapour-diffusion method. The orthorhombic crystals have unit-cell dimensions of a = 92.5, b = 125.4, c = 192.1 A; alpha = beta = gamma = 90 degrees. The crystals diffract beyond 4 A on a 1.08 A synchrotron radiation source
-
using 0.2 M ammonium sulfate, 0.1 M Na-cacodylate (pH 6.5), 5 mM dithiothreitol, 50 mM MnCl2, and 15% (w/v) PEG 8000
crystals are grown at 20°C according to the hanging-drop vapor-diffusion method. The N-terminal (1-300) domain structure of the large subunit was determined by X-ray crystallography, although about 50 N-terminal residues are disordered. The determined structure consists of nine alpha helices and three beta strands. The DNA-binding ability of the domain by is identified by SPR measurement. The N-terminal (1-100) region plays crucial roles in the folding of the large subunit dimer by connecting the about 50 N-terminal residues with their own catalytic region (792-1163)
hanging-drop vapor-diffusion method at 20°C, the N-terminal (1–300) domain structure of the large subunit was determined by X-ray crystallography. The determined structure consists of nine alpha helices and three beta strands. The N-terminal (1–100) region plays crucial roles in the folding of the large subunit dimer by connecting the about 50 N-terminal residues with their own catalytic region (792–1163)
sitting-drop vapor diffusion method, apo form at 2.5 A resolution, crystals belong to the space group P212121, with unit-cell parameters a: 77.0, b: 112.0, c: 111.8 A
31000 MW C-terminal fragment of rat DNA polymerase beta, microdialysis
-
crystal structure of catalytic domain of rat DNA polymerase beta, hanging drop vapor diffusion method
-
DNA polymerase beta
-
2.3 A resolution crystal structure of a catalytic fragment
2.8 A resolution crystal structure
bypass crystal structures of Dpo4:DNA(S-cdG):dCTP (error-free) and Dpo4:DNA(S-cdG):dTTP (error-prone) are catalytically incompetent. In Dpo4:DNA(S-cdG):dTTP structure, S-cdG induces a loop structure and causes an unusual 5'-template base clustering at the active site, providing the first structural evidence for the previously suggested template loop structure that can be induced by a cyclopurine lesion
crystal data and refinement parameters for the ternary (protein/DNA/GTP) complexes of Dpo4, The complexes are crystallized by sitting-drop vapor diffusion
-
crystal forms for the N249Y mutant enzyme are obtained at 22°C by the microbatch method
crystal structure of Dpo4 in complex with North-methanocarba-dATP opposite dT
crystal structure of ternary complex Dpo4/blunt-end DNA/dATP, crystals are produced by the hanging-drop method at 20°C
crystal structures of Dpo4 complexes with oligonucleotides are solved with C, A, and G nucleoside triphosphates placed opposite 8-oxoG
crystal structures of Dpo4 in complex with DNA duplexes containing the 2,4-difluorotoluene analog. The structures provide insight into the discrimination by Dpo4 between dATP and dGTP opposite 2,4-difluorotoluene and its inability to extend beyond a G:2,4-difluorotoluene pair
crystallization of an enzyme:DNA complex, sitting drop vapor diffusion method by mixing 0.001 mL of complex with 0.001 mL of a solution containing 50 mM Tris-HCl (pH 7.4 at 25°C) buffer, 12-20% polyethylene glycol 3350 (w/v), 100 mM Ca(OAc)2, and 2.5% glycerol (v/v)
crystallization of enzyme-DNA complexes
crystallization of mutant enzymes R332A and R332E in complex with DNA and dGTP (R332E(8-oxoG:A), R332E(8-oxoG:C), R332A(8-oxoG:A) and R332A(8-oxoG:C)). The R332E(8-oxoG:C) structure is crystallized by the hanging drop vapor diffusion technique, using a mixture of 14% polyethylene glycol 4000 (w/v), 0.1 M calcium acetate, and 20 mM HEPES (pH 7.3) as reservoir
crystals are generated by the vapour diffusion in hanging drops. Crystal structure of the full-length enzyme Dpo4 in complex with heterodimeric sliding clamp PCNA1–PCNA2 at 2.05 A resolution. Two hinges render the multidomain polymerase flexible conformations and orientations relative to PCNA. The enzyme binds specifically to PCNA1 on the conserved ligand binding site
crystals are grown at room temperature by hanging drop vapor diffusion
crystals are grown using the sitting drop vapor diffusion method (pH 7.4 , 25°C). The Dpo4 polymerase is cocrystallized with the aflatoxin B1-formamidopyrimidine-modified template and the structure is determined at 3.0 A resolution. The structures of the ternary complexes are determined at 2.9 and 2.7 A resolutions for the dATP and dTTP complexes, respectively
determination of crystal structures of a binary Mg2+-form Dpo4–DNA complex with 1,N2-etheno-dG in the template strand as well as of ternary Mg2+-form Dpo4–DNA–dCTP/dGTP complexes with 8-oxoG in the template strand. Crystals are grown using the sitting-drop vapor-diffusion method by mixing equal amounts of Dpo4–DNA complex solution and of a reservoir solution containing 12–20% polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M magnesium acetate and 20 mMTris pH 7.5
Dpo4 in complex with DNA duplex containing N2,N2-dimethyl-substituted guanine-modified template, sitting drop vapor diffusion method, using 10-15% polyethylene glycol 3350 (w/v), 30 mM NaCl, 100 mM MgCl2, and 3% glycerol (v/v)
hanging drop method, crystals of the enzyme in complexes with DNA (the binary complex) in the presence or absence of an incoming nucleotide are analyzed by Raman microscopy. 13C- and 15N-labeled d*CTP, or unlabeled dCTP, are soaked into the binary crystals with G as the templating base. In the presence of the catalytic metal ions, Mg2+ and Mn2+, nucleotide incorporation is detected by the disappearance of the triphosphate band of dCTP and the retention of *C modes in the crystal following soaking out of noncovalently bound C(or *C)TP. The addition of the second coded base, thymine, is observed by adding cognate dTTP to the crystal following a single d*CTP addition. Adding these two bases caused visible damage to the crystal that is possibly caused by protein and/or DNA conformational change within the crystal. When d*CTP is soaked into the Dpo4 crystal in the absence of Mn2+ or Mg2+, the primer extension reaction does not occur. Instead, a ternary protein/template/d*CTP complex is formed
hanging-drop vapor diffusion method at 20°C
hanging-drop vapor diffusion method at 20°C, crystal structures of the enzyme in ternary complexes with DNA and an incoming nucleotide, either correct or incorrect, solved at 1.7 A and 2.1 A resolution, respectively
hanging-drop vapour-diffusion method at 21°C using ammonium sulfate as precipitant. The crystals belong to the monoclinic space group C2 with cell dimensions a = 187.4, b = 68.5, c = 125.8 A and beta = 107.8 degrees and diffract up to 2.7 A resolution
hanging-drop vapour-diffusion method at 21°C using ammonium sulfate as precipitant. The crystals belong to the monoclinic space group C2 with cell dimensions a = 187.4, b = 68.5, c = 125.8 A and beta = 107.8 degrees and diffract up to 2.7 A resolution on a rotating-anode X-ray source
sitting drop vapor diffusion method, crystallization of Dpo4/(6S,8R,11S)-trans-4-hydroxynonenal-dGuo modified 18-mer template primer DNA complexes
sitting drop vapor diffusion method, crystallization of Dpo4/DNA complexes. Crystal structures reveal wobble pairing between C and O6-BzG
-
sitting drop vapor diffusion method, the crystal structure of DNA polymerase complexed with mirror (DNADpo4/l-DNA complex) reveals a dimer formed by the little finger domain that provides a binding site for l-DNA
sitting drop, vapor-diffusion method with the reservoir solution containing 10–15% polyethylene glycol 3350 (w/v), 30 mm NaCl, 100 mm MgCl2, and 3% glycerol (v/v). One crystal structure of Dpo4 with a primer having a 3'-terminal dideoxycytosine opposite template N2,N2-dimethylguanine in a post-insertion position shows dideoxycytosine folded back into the minor groove, as a catalytically incompetent complex. A second crystal has two unique orientations for the primer terminal dideoxycytosine as follows: (I) flipped into the minor groove and (II) a long pairing with N2,N2-dimethylguanine in which one hydrogen bond exists between the O-2 atom of dideoxycytosine and the N-1 atom of N2,N2-dimethylguanine, with a second water-mediated hydrogen bond between the N-3 atom of dideoxycytosine and the O-6 atom of N2,N2-dimethylguanine. A crystal structure of Dpo4 with dTTP opposite template N2,N2-dimethylguanine reveals a wobble orientation
ternary enzyme/DNA/dNTP complexes
ternary polymerase-DNA-dNTP, dGTP and/or dATP, complexes for three template-primer DNA sequences, 18-mer-primer 13-mer sequences containing 1,N2-propanodeoxyguanosine, with bound Ca2+, X-ray diffraction structure determination and analysis at 2.4-2.7 A resolution, modelling
the enzyme is mixed with DNA (1:1.2 molar ratio) in 20 mM Tris-HCl buffer (pH 8.0, 25 °C) containing 60 mM NaCl, 4% glycerol (v/v), and 5 mM 2-mercaptoethanol and then placed on ice for 1 h prior to incubation with 5 mM MgCl2 and 1 mM dGTP. Crystals are grown using the sitting drop/vapor-diffusion method with the reservoir solution containing 20 mM Tris-HCl (pH 8.0 at 25 °C), 15% polyethylene glycol 3350 (w/v), 60 mM NaCl, 5 mM MgCl2, and 4% glycerol (v/v). Two crystal structures of Dpo4 with a template N2-NaphG (in a post-insertion register opposite a 3-terminal C in the primer) are solved. One shows N2-NaphG in a syn conformation, with the naphthyl group located between the template and the Dpo4 “little finger” domain. The Hoogsteen face is within hydrogen bonding distance of the N4 atoms of the cytosine opposite N2-NaphG and the cytosine at the 2 position. The second structure shows N2-NaphG in an anti conformation with the primer terminus largely disordered
the structure of the enzyme bound to G*T-mispaired primer template in the presence of an incoming nucleotide is solved. As a control the structure of the enzyme bound to a matched A-T base pair at the primer terminus is also determined. The structures offer a basis for the low efficiency of the enzyme in extending a G*T mispair: a reverse wobble that deflects the primer 3'-OH away from the incoming nucleotide
three crystal structures of a the enzyme in complex with Pt-GG DNA (1,2-intrastrand covalent linkage, cis-Pt-1,2-d(GpG)) at 2.9, 1.9, and 2.0 A resolution, respectively. The crystallographic snapshots show three stages of lesion bypass: the nucleotide insertions opposite the 3'G (first insertion) and 5'G (second insertion) of Pt-GG, and the primer extension beyond the lesion site
X-ray structure, 2.4 A resolution
crystals of mutant enzyme K242R/I243K/P244S are grown at room temperature by hanging-drop vapor diffusion, 2.4 A resolution crystal structure
structure-function analysis of the pRN1 primase-polymerase domain. The crystal structure shows a central depression lined by conserved residues. Mutations on one side of the depression reduce DNA affinity. On the opposite side of the depression cluster three acidic residues and a histidine, which are required for primase and DNA polymerase activity. One acidic residue binds a manganese ion, suggestive of a metal-dependent catalytic mechanism. The structure does not show any similarity to DNA polymerases, but is distantly related to archaeal and eukaryotic primases, with corresponding active-site residues
sitting-drop vapor-diffusion technique at 4°C, 2.5 A resolution crystal structure
hanging drop method. The Thumb domain of DNA polymerase shows an opened conformation. The fingers subdomain possesses many basic residues at the side of the polymerase active site. The residues are considered to be accessible to the incoming dNTP by electrostatic interaction. A beta-hairpin motif (residues 242-249) extends from the exonuclease domain as seen in the editing complex of the RB69 DNA polymerase from bacteriophage RB69. Many arginine residues are located at the forked-point (the junction of the template-binding and editing clefts) of KOD DNA polymerase, suggesting that the basic environment is suitable for partitioning of the primer and template DNA duplex and for stabilizing the partially melted DNA structure in the high-temperature environments
hanging drop vapor diffusion technique
-
hanging-drop vapor diffusion method, crystal structure of Thermus aquaticus DNA polymerase III alpha subunit reveals that the structure of the catalytic domain of the eubacterial replicative polymerase is unrelated to that of the eukaryotic replicative polymerase but rather belongs to the Polbeta-like nucleotidyltransferase superfamily