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- PDB-6p7e: Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and... -

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Basic information

Entry
Database: PDB / ID: 6p7e
TitleStructure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase
Components
  • ASP-THR-ASP-PHE peptide
  • DNA (25-MER)
  • DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')
  • DNA-directed DNA polymerase
  • THR-ASP-PHE peptide
  • TrxA
KeywordsTRANSFERASE/DNA BINDING PROTEIN/DNA / DNA Replication / DNA polymerase / DNA binding protein / TRANSFERASE-DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA synthesis involved in DNA replication / DNA exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA polymerase processivity factor activity / protein-disulfide reductase activity / 3'-5' exonuclease activity / cell redox homeostasis / DNA-templated DNA replication / double-strand break repair ...DNA synthesis involved in DNA replication / DNA exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA polymerase processivity factor activity / protein-disulfide reductase activity / 3'-5' exonuclease activity / cell redox homeostasis / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DNA-directed DNA polymerase T7 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Thioredoxin / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain ...DNA-directed DNA polymerase T7 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Thioredoxin / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Ribonuclease H-like superfamily/Ribonuclease H / Glutaredoxin / Glutaredoxin / Nucleotidyltransferase; domain 5 / Thioredoxin-like superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase / Thioredoxin 1 / Thioredoxin
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.001 Å
AuthorsFoster, B.M. / Rosenberg, D. / Salvo, H. / Stephens, K.L. / Bintz, B.J. / Hammel, M. / Ellenberger, T. / Gainey, M.D. / Wallen, J.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM055390 United States
CitationJournal: Biochemistry / Year: 2019
Title: Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome.
Authors: Foster, B.M. / Rosenberg, D. / Salvo, H. / Stephens, K.L. / Bintz, B.J. / Hammel, M. / Ellenberger, T. / Gainey, M.D. / Wallen, J.R.
History
DepositionJun 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed DNA polymerase
B: DNA-directed DNA polymerase
C: DNA-directed DNA polymerase
D: DNA-directed DNA polymerase
E: TrxA
F: TrxA
G: TrxA
H: TrxA
I: DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')
J: DNA (25-MER)
K: DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')
L: DNA (25-MER)
M: DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')
N: DNA (25-MER)
O: DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')
P: DNA (25-MER)
U: ASP-THR-ASP-PHE peptide
V: ASP-THR-ASP-PHE peptide
W: THR-ASP-PHE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,89239
Polymers423,74319
Non-polymers4,14920
Water55831
1
A: DNA-directed DNA polymerase
E: TrxA
I: DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')
J: DNA (25-MER)
U: ASP-THR-ASP-PHE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,12610
Polymers106,0895
Non-polymers1,0375
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-directed DNA polymerase
F: TrxA
K: DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')
L: DNA (25-MER)
V: ASP-THR-ASP-PHE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,12610
Polymers106,0895
Non-polymers1,0375
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA-directed DNA polymerase
G: TrxA
M: DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')
N: DNA (25-MER)
W: THR-ASP-PHE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,01110
Polymers105,9745
Non-polymers1,0375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-77 kcal/mol
Surface area40570 Å2
MethodPISA
4
D: DNA-directed DNA polymerase
H: TrxA
O: DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')
P: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6299
Polymers105,5924
Non-polymers1,0375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-63 kcal/mol
Surface area39790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.724, 102.698, 148.885
Angle α, β, γ (deg.)91.36, 96.83, 113.11
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
DNA-directed DNA polymerase / Gene product 5 / Gp5


Mass: 79703.578 Da / Num. of mol.: 4 / Mutation: D5A, E7A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P00581, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters
#2: Protein
TrxA / Thioredoxin 1


Mass: 11818.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA / Production host: Escherichia coli (E. coli) / Variant (production host): HMS174(DE3) / References: UniProt: Q14F07, UniProt: P0AA25*PLUS

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DNA chain , 2 types, 8 molecules IKMOJLNP

#3: DNA chain
DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')


Mass: 6551.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T7 (virus)
#4: DNA chain
DNA (25-MER)


Mass: 7518.855 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T7 (virus)

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Protein/peptide , 2 types, 3 molecules UVW

#5: Protein/peptide ASP-THR-ASP-PHE peptide


Mass: 496.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T7 (virus)
#6: Protein/peptide THR-ASP-PHE peptide


Mass: 381.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T7 (virus)

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Non-polymers , 3 types, 51 molecules

#7: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→49.129 Å / Num. obs: 107350 / % possible obs: 98.8 % / Redundancy: 3.7 % / Net I/σ(I): 7.64
Reflection shellResolution: 3→3.03 Å / Num. unique obs: 3336

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJQ

2ajq


Resolution: 3.001→49.129 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.33
RfactorNum. reflection% reflection
Rfree0.2481 5354 4.99 %
Rwork0.2142 --
obs0.2159 107350 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.001→49.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24899 3773 128 31 28831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00629827
X-RAY DIFFRACTIONf_angle_d1.17241171
X-RAY DIFFRACTIONf_dihedral_angle_d12.29716975
X-RAY DIFFRACTIONf_chiral_restr0.0624420
X-RAY DIFFRACTIONf_plane_restr0.0094651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0007-3.03470.4221820.40033336X-RAY DIFFRACTION95
3.0347-3.07040.3861610.36063325X-RAY DIFFRACTION98
3.0704-3.10790.37411840.34053445X-RAY DIFFRACTION99
3.1079-3.14720.36751800.32173371X-RAY DIFFRACTION99
3.1472-3.18860.34832080.29553346X-RAY DIFFRACTION99
3.1886-3.23230.3271640.27613413X-RAY DIFFRACTION98
3.2323-3.27850.31071880.27063394X-RAY DIFFRACTION99
3.2785-3.32740.31511610.26823435X-RAY DIFFRACTION99
3.3274-3.37940.27931900.26353379X-RAY DIFFRACTION99
3.3794-3.43480.28741730.25763389X-RAY DIFFRACTION99
3.4348-3.4940.32321970.25453365X-RAY DIFFRACTION99
3.494-3.55750.31051620.25123434X-RAY DIFFRACTION99
3.5575-3.62590.30771730.24613409X-RAY DIFFRACTION99
3.6259-3.69990.29011640.23083421X-RAY DIFFRACTION99
3.6999-3.78030.28651760.22383413X-RAY DIFFRACTION99
3.7803-3.86820.21611760.21193459X-RAY DIFFRACTION99
3.8682-3.96490.23071890.21023347X-RAY DIFFRACTION99
3.9649-4.07210.23811610.19493428X-RAY DIFFRACTION99
4.0721-4.19180.23091920.1873402X-RAY DIFFRACTION99
4.1918-4.3270.20331710.17043430X-RAY DIFFRACTION99
4.327-4.48160.18542130.17033401X-RAY DIFFRACTION99
4.4816-4.66090.19471910.17343375X-RAY DIFFRACTION99
4.6609-4.87280.231940.18163398X-RAY DIFFRACTION99
4.8728-5.12950.20381980.17943441X-RAY DIFFRACTION99
5.1295-5.45050.2321740.18683379X-RAY DIFFRACTION99
5.4505-5.87070.22861770.19223415X-RAY DIFFRACTION99
5.8707-6.46030.2341790.19073430X-RAY DIFFRACTION99
6.4603-7.39240.21911650.18723443X-RAY DIFFRACTION99
7.3924-9.30330.17881680.16173428X-RAY DIFFRACTION99
9.3033-49.1360.18881430.19233345X-RAY DIFFRACTION97

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