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

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Basic information

Entry
Database: PDB / ID: 1jql
TitleMechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of beta-delta (1-140)
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 clamp loader activity / DNA polymerase III complex / 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 clamp loader activity / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation / 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 / 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 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 / 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 / : / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.0Sep 26, 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 1.6Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_database_related
Item: _pdbx_database_related.db_name

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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, DELTA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)56,1132
Polymers56,1132
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-11 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.1, 110.1, 134.9
Angle α, β, γ (deg.)90, 90, 120
Int Tables number150
Space group name H-MP321

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Components

#1: Protein DNA Polymerase III, BETA CHAIN


Mass: 40546.352 Da / Num. of mol.: 1 / 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: 15566.679 Da / Num. of mol.: 1 / Fragment: Amino Terminal (1-140) domain
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: 4.2 Å3/Da / Density % sol: 70.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: TRIS-HCL, polyethylene glycol 4000, MgCl2, dithiothreitol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein11
250 mMTris-HCl11
310-11 %PEG400011
4100 mM11MgCl2
52 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 5, 2000
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→500 Å / Num. obs: 36450 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Rsym value: 0.08
Reflection
*PLUS
Lowest resolution: 500 Å / Num. measured all: 740503 / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model of the beta-delta complex of DNA Polymerase III

Resolution: 2.5→500 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2527 8.8 %Random
Rwork0.249 ---
all-36450 --
obs-28777 98.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 0 0 3932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.62846
X-RAY DIFFRACTIONc_bond_d0.008919
Refinement
*PLUS
Lowest resolution: 500 Å / Rfactor obs: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS

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