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- PDB-2g4c: Crystal Structure of human DNA polymerase gamma accessory subunit -

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Basic information

Entry
Database: PDB / ID: 2g4c
TitleCrystal Structure of human DNA polymerase gamma accessory subunit
ComponentsDNA polymerase gamma subunit 2
KeywordsTRANSFERASE / alpha and beta protein / anti-codon binding domain-like / aaRS class II-like
Function / homology
Function and homology information


gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / mitochondrial nucleoid / DNA polymerase binding / Transcriptional activation of mitochondrial biogenesis / DNA-templated DNA replication / double-stranded DNA binding / in utero embryonic development ...gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / mitochondrial nucleoid / DNA polymerase binding / Transcriptional activation of mitochondrial biogenesis / DNA-templated DNA replication / double-stranded DNA binding / in utero embryonic development / DNA-directed DNA polymerase activity / mitochondrial matrix / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
POLG2, C-terminal / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold ...POLG2, C-terminal / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA polymerase subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsFan, L. / Farr, C.L. / Kaguni, L.S. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase
Authors: Fan, L. / Kim, S. / Farr, C.L. / Schaefer, K.T. / Randolph, K.M. / Tainer, J.A. / Kaguni, L.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE Residue 169 is a Thr according to Carrodeguas and Bogenhagen, 2000, Nucleic Acids Res. 28, ...SEQUENCE Residue 169 is a Thr according to Carrodeguas and Bogenhagen, 2000, Nucleic Acids Res. 28, 1237-1244. The sequence in the deposition agrees with the reference

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase gamma subunit 2
B: DNA polymerase gamma subunit 2
C: DNA polymerase gamma subunit 2
D: DNA polymerase gamma subunit 2


Theoretical massNumber of molelcules
Total (without water)215,6304
Polymers215,6304
Non-polymers00
Water55831
1
A: DNA polymerase gamma subunit 2
C: DNA polymerase gamma subunit 2


Theoretical massNumber of molelcules
Total (without water)107,8152
Polymers107,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-39 kcal/mol
Surface area36190 Å2
MethodPISA
2
B: DNA polymerase gamma subunit 2
D: DNA polymerase gamma subunit 2


Theoretical massNumber of molelcules
Total (without water)107,8152
Polymers107,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-39 kcal/mol
Surface area36190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.790, 101.790, 170.277
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThe biological assembly is likely a homodimer.

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Components

#1: Protein
DNA polymerase gamma subunit 2 / Mitochondrial DNA polymerase accessory subunit / PolG-beta / MtPolB / DNA polymerase gamma ...Mitochondrial DNA polymerase accessory subunit / PolG-beta / MtPolB / DNA polymerase gamma accessory 55 kDa subunit / p55


Mass: 53907.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLG2, MTPOLB / Plasmid: pQESL-Hp55 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UHN1, DNA-directed DNA polymerase
#2: 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 10%PEG 8000, 100 mM Tris-Cl, pH 8.0, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2004
RadiationMonochromator: Si(iii) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 34088 / Num. obs: 33633 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 16.7
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 1.94 / Num. unique all: 3386 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G5H

1g5h


Resolution: 3.15→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.285 1610 random
Rwork0.232 --
all0.217 34088 -
obs0.217 32261 -
Refinement stepCycle: LAST / Resolution: 3.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12816 0 0 31 12847
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_bond_d0.0078
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param

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