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- PDB-3ikm: Crystal structure of human mitochondrial DNA polymerase holoenzyme -

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Basic information

Entry
Database: PDB / ID: 3ikm
TitleCrystal structure of human mitochondrial DNA polymerase holoenzyme
Components
  • DNA polymerase subunit gamma-1
  • DNA polymerase subunit gamma-2
KeywordsTRANSFERASE / Human mitochondrial DNA polymerase / Disease mutation / DNA replication / DNA-binding / DNA-directed DNA polymerase / Magnesium / Mitochondrion / Neuropathy / Nucleotidyltransferase / Progressive external ophthalmoplegia / Transit peptide
Function / homology
Function and homology information


gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / DNA polymerase processivity factor activity / mitochondrial nucleoid / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / DNA polymerase processivity factor activity / mitochondrial nucleoid / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / DNA polymerase binding / base-excision repair, gap-filling / 3'-5' exonuclease activity / Transcriptional activation of mitochondrial biogenesis / DNA-templated DNA replication / double-stranded DNA binding / in utero embryonic development / protease binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / intracellular membrane-bounded organelle / chromatin binding / protein-containing complex / mitochondrion / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
Nucleotidyltransferase; domain 5 - #390 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3960 / DNA-directed DNA-polymerase, family A, mitochondria / DNA mitochondrial polymerase, exonuclease domain / : / DNA mitochondrial polymerase exonuclease domain / POLG2, C-terminal / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / DNA polymerase family A ...Nucleotidyltransferase; domain 5 - #390 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3960 / DNA-directed DNA-polymerase, family A, mitochondria / DNA mitochondrial polymerase, exonuclease domain / : / DNA mitochondrial polymerase exonuclease domain / POLG2, C-terminal / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / DNA polymerase family A / Anticodon-binding / Anticodon binding domain / 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 / 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) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Nucleotidyltransferase; domain 5 / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase subunit gamma-1 / DNA polymerase subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.24 Å
AuthorsLee, Y.-S. / Kennedy, W.D. / Yin, Y.W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Structural insight into processive human mitochondrial DNA synthesis and disease-related polymerase mutations.
Authors: Lee, Y.S. / Kennedy, W.D. / Yin, Y.W.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase subunit gamma-1
B: DNA polymerase subunit gamma-2
C: DNA polymerase subunit gamma-2
D: DNA polymerase subunit gamma-1
E: DNA polymerase subunit gamma-2
F: DNA polymerase subunit gamma-2


Theoretical massNumber of molelcules
Total (without water)459,8016
Polymers459,8016
Non-polymers00
Water0
1
A: DNA polymerase subunit gamma-1
B: DNA polymerase subunit gamma-2
C: DNA polymerase subunit gamma-2


Theoretical massNumber of molelcules
Total (without water)229,9003
Polymers229,9003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-21.1 kcal/mol
Surface area38320 Å2
MethodPISA
2
D: DNA polymerase subunit gamma-1
E: DNA polymerase subunit gamma-2
F: DNA polymerase subunit gamma-2


Theoretical massNumber of molelcules
Total (without water)229,9003
Polymers229,9003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-19.8 kcal/mol
Surface area38270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.394, 138.394, 226.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsTHE BIOLOGICAL UNIT (HOLOENZYME) CONTAINS ONE MONOMERIC CATALYTIC SUBUNIT AND ONE DIMERIC ACCESSORY SUBUNIT.

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Components

#1: Protein DNA polymerase subunit gamma-1 / / Mitochondrial DNA polymerase catalytic subunit / PolG-alpha


Mass: 132384.688 Da / Num. of mol.: 2 / Fragment: UNP residues 70-1239 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P54098, DNA-directed DNA polymerase
#2: Protein
DNA polymerase subunit gamma-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: 48757.902 Da / Num. of mol.: 4 / Fragment: UNP residues 59-485 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UHN1, DNA-directed DNA polymerase
Sequence detailsTHE SEQUENCE PROVIDED BY AUTHORS DOES NOT AGREE WITH THE SEQUENCE IN COORDINATES, AND ALSO DOES NOT ...THE SEQUENCE PROVIDED BY AUTHORS DOES NOT AGREE WITH THE SEQUENCE IN COORDINATES, AND ALSO DOES NOT MATCH THE UNIPROT DATABASE. THE FOLLOWING RESIDUES ARE LINKED TOGETHER IN COORDINATES: (A PRO 370) AND (A LYS 371) (B PRO 137) AND (B GLY 179) (C ARG 146) AND (C SER 178) (D ASN 354) AND (D SER 355) (E PRO 137) AND (E GLY 179) (F ARG 146) AND (F SER 178)

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.24→47 Å / Num. obs: 76584 / % possible obs: 99 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.24→46.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 41884.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.303 3275 4.8 %RANDOM
Rwork0.284 ---
obs0.284 68650 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2435 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 83.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å20 Å2
2---2.33 Å20 Å2
3---4.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.85 Å0.86 Å
Luzzati d res low-5 Å
Luzzati sigma a1.14 Å0.74 Å
Refinement stepCycle: LAST / Resolution: 3.24→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29480 0 0 0 29480
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.97
Refine LS restraints NCSNCS model details: NONE
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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