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- PDB-1jqj: Mechanism of Processivity Clamp Opening by the Delta Subunit Wren... -

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Basic information

Entry
Database: PDB / ID: 1jqj
TitleMechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex
Components
  • DNA polymerase III, beta chain
  • DNA polymerase III, delta subunit
KeywordsTRANSFERASE / DNA Polymerase / Processivity Clamp / Clamp Loader / DNA Replication / AAA+ ATPase
Function / homology
Function and homology information


DNA polymerase III, clamp loader complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / DNA clamp loader activity / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis ...DNA polymerase III, clamp loader complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / DNA clamp loader activity / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA damage response / protein homodimerization activity / DNA binding / identical protein binding / cytosol
Similarity search - Function
DNA polymerase III subunit delta, C-terminal / Processivity clamp loader gamma complex DNA pol III C-term / DNA polymerase III, delta subunit / DNA polymerase III delta, N-terminal / : / DNA polymerase III, delta subunit / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 ...DNA polymerase III subunit delta, C-terminal / Processivity clamp loader gamma complex DNA pol III C-term / DNA polymerase III, delta subunit / DNA polymerase III delta, N-terminal / : / DNA polymerase III, delta subunit / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Helicase, Ruva Protein; domain 3 - #60 / : / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Beta sliding clamp / DNA polymerase III subunit delta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsJeruzalmi, D. / Yurieva, O. / Zhao, Y. / Young, M. / Stewart, J. / Hingorani, M. / O'Donnell, M. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III.
Authors: Jeruzalmi, D. / Yurieva, O. / Zhao, Y. / Young, M. / Stewart, J. / Hingorani, M. / O'Donnell, M. / Kuriyan, J.
History
DepositionAug 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III, beta chain
B: DNA polymerase III, beta chain
C: DNA polymerase III, delta subunit
D: DNA polymerase III, delta subunit


Theoretical massNumber of molelcules
Total (without water)158,5844
Polymers158,5844
Non-polymers00
Water00
1
A: DNA polymerase III, beta chain
C: DNA polymerase III, delta subunit


Theoretical massNumber of molelcules
Total (without water)79,2922
Polymers79,2922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-9 kcal/mol
Surface area34120 Å2
MethodPISA
2
B: DNA polymerase III, beta chain
D: DNA polymerase III, delta subunit


Theoretical massNumber of molelcules
Total (without water)79,2922
Polymers79,2922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: DNA polymerase III, beta chain
C: DNA polymerase III, delta subunit

B: DNA polymerase III, beta chain
D: DNA polymerase III, delta subunit


Theoretical massNumber of molelcules
Total (without water)158,5844
Polymers158,5844
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
Buried area11650 Å2
ΔGint-37 kcal/mol
Surface area60780 Å2
MethodPISA
4
D: DNA polymerase III, delta subunit

A: DNA polymerase III, beta chain
C: DNA polymerase III, delta subunit


Theoretical massNumber of molelcules
Total (without water)118,0383
Polymers118,0383
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_545x+1/2,y-1/2,z1
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-22 kcal/mol
Surface area47920 Å2
MethodPISA
5
C: DNA polymerase III, delta subunit

B: DNA polymerase III, beta chain
D: DNA polymerase III, delta subunit


Theoretical massNumber of molelcules
Total (without water)118,0383
Polymers118,0383
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_455x-1/2,y+1/2,z1
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-18 kcal/mol
Surface area47780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.836, 99.293, 113.023
Angle α, β, γ (deg.)90.0, 119.165, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA polymerase III, beta chain


Mass: 40546.352 Da / Num. of mol.: 2 / Mutation: I272A, L273A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A988, DNA-directed DNA polymerase
#2: Protein DNA polymerase III, delta subunit


Mass: 38745.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P28630, DNA-directed DNA polymerase

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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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: TRIS, Ammonium phosphate, dithiothreitol, ammonium tartartate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 2, 2001
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→500 Å / Num. obs: 42243 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.11

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→500 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3079 1922 5 %Random
Rwork0.2658 ---
all-43706 --
obs-38197 --
Refinement stepCycle: LAST / Resolution: 2.9→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10860 0 0 0 10860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.67811
X-RAY DIFFRACTIONc_bond_d0.009807
X-RAY DIFFRACTIONc_mcbond_it1.463
X-RAY DIFFRACTIONc_mcangle_it2.692
X-RAY DIFFRACTIONc_scbond_it1.544
X-RAY DIFFRACTIONc_scangle_it2.691

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