4M9N

DNA Polymerase Beta E295K Soaked with dATP

> Summary

Summary for 4M9N

Related4M9G 4M9H 4M9J 4M9L
DescriptorDNA polymerase beta (E.C.2.7.7.7, 4.2.99.-)
Functional Keywordsdna polymerase, lyase, dna complex, transferase-dna complex, transferase/dna
Biological sourceHomo sapiens (human)
More
Cellular locationNucleus P06746
Total number of polymer chains4
Total molecular weight48253.86
Authors
Eckenroth, B.E.,Doublie, S. (deposition date: 2013-08-14, release date: 2013-10-16, modification date: 2013-12-18)
Primary citation
Eckenroth, B.E.,Towle-Weicksel, J.B.,Sweasy, J.B.,Doublie, S.
The E295K Cancer Variant of Human Polymerase beta Favors the Mismatch Conformational Pathway during Nucleotide Selection.
J.Biol.Chem., 288:34850-34860, 2013
PubMed: 24133209
DOI: 10.1074/jbc.M113.510891
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.275 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.239201.2%2.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4m9n
no rotation
Molmil generated image of 4m9n
rotated about x axis by 90°
Molmil generated image of 4m9n
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ADNA polymerase betapolymer33538242.11
UniProt (P06746)
Pfam (PF10391)
Pfam (PF14716)
Pfam (PF14791)
Pfam (PF14792)
Homo sapiens (human)@PDBj
TDNA Template Strandpolymer164853.21
PDNA Primer Strandpolymer103061.01
DDNA Downstream Strandpolymer51536.01
SODIUM IONnon-polymer23.02
MAGNESIUM IONnon-polymer24.31
2'-DEOXYADENOSINE 5'-TRIPHOSPHATEnon-polymer491.21
waterwater18.0234

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight47692.4
Non-Polymers*Number of molecules4
Total molecular weight561.5
All*Total molecular weight48253.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.275 Å)

Cell axes54.52379.21554.685
Cell angles90.00106.2490.00
SpacegroupP 1 21 1
Resolution limits13.92 - 2.28
the highest resolution shell value2.305 - 2.275
R-factor0.1951
R-work0.19150
the highest resolution shell value0.250
R-free0.22670
the highest resolution shell value0.315
RMSD bond length0.002
RMSD bond angle0.598

Data Collection Statistics

Resolution limits14.00 - 2.28
the highest resolution shell value -
Rmerge_l_obs0.053
the highest resolution shell value0.245
Completeness97.5
Redundancy3.3
the highest resolution shell value2.3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1vapor diffusion, hanging drop7.5291

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0005874cellular_componentmicrotubule
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0043234cellular_componentprotein complex
A0005876cellular_componentspindle microtubule
A0003684molecular_functiondamaged DNA binding
A0003906molecular_functionDNA-(apurinic or apyrimidinic site) lyase activity
A0003887molecular_functionDNA-directed DNA polymerase activity
A0019899molecular_functionenzyme binding
A0016829molecular_functionlyase activity
A0046872molecular_functionmetal ion binding
A0008017molecular_functionmicrotubule binding
A0007568biological_processaging
A0006284biological_processbase-excision repair
A0006286biological_processbase-excision repair, base-free sugar-phosphate removal
A0006288biological_processbase-excision repair, DNA ligation
A0006287biological_processbase-excision repair, gap-filling
A0006974biological_processcellular response to DNA damage stimulus
A0006281biological_processDNA repair
A0006261biological_processDNA-dependent DNA replication
A0048872biological_processhomeostasis of number of cells
A0071707biological_processimmunoglobulin heavy chain V-D-J recombination
A0006954biological_processinflammatory response
A0008630biological_processintrinsic apoptotic signaling pathway in response to DNA damage
A0048535biological_processlymph node development
A0051402biological_processneuron apoptotic process
A0006290biological_processpyrimidine dimer repair
A0045471biological_processresponse to ethanol
A0010332biological_processresponse to gamma radiation
A0055093biological_processresponse to hyperoxia
A0007435biological_processsalivary gland morphogenesis
A0016446biological_processsomatic hypermutation of immunoglobulin genes
A0048536biological_processspleen development
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16BINDING SITE FOR RESIDUE NA A 401
ChainResidue
ATHR101
AVAL103
AILE106
AHOH
PDG9
PHOH

AC26BINDING SITE FOR RESIDUE NA A 402
ChainResidue
ALYS60
ALEU62
AVAL65
AHOH
DDC3
DHOH

AC35BINDING SITE FOR RESIDUE MG A 403
ChainResidue
AASP190
AASP192
ADTP
AHOH
AHOH

AC417BINDING SITE FOR RESIDUE DTP A 404
ChainResidue
AARG149
ASER180
AARG183
AGLY189
AASP190
AASP192
ATYR271
APHE272
ATHR273
AGLY274
AASP276
AASN279
AMG
AHOH
AHOH
AHOH
PDC10

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
DTP_4m9n_A_404182'-DEOXYADENOSINE 5'-TRIPHOSPHATE binding site
ChainResidueligand
AARG149DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
AGLY179-SER180DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
AARG183DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ASER187-ASP190DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
AASP192DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ATYR271-ASP276DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
AASN279DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
TDA6DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
PDC10DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Schiff-base intermediate with DNA.
ChainResidueDetails
ALYS72

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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