BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 27409

Title: Ile and Met methyl 1H and 13C chemical shifts of DNA polymerase beta and 1-nucleotide gapped double hairpin DNA binary complex   PubMed: 29917149

Authors: DeRose, Eugene; Kirby, Thomas; Mueller, Geoffrey; Beard, William; Wilson, Samuel; London, Robert

Citation: DeRose, Eugene; Kirby, Thomas; Mueller, Geoffrey; Beard, William; Wilson, Samuel; London, Robert. "Transitions in DNA polymerase beta microsecond-millisecond dynamics related to substrate binding and catalysis"  Nucleic Acids Res. 46, 7309-7322 (2018).

Assembly members:
DNA_polymerase_beta_polypeptide, polymer, 335 residues, Formula weight is not available
1-nucleotide_gapped_double_hairpin_DNA, polymer, 23 residues, Formula weight is not available
entity_MG, non-polymer, 24.305 Da.

Natural source:   Common Name: Rat   Taxonomy ID: 10116   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Rattus norvegicus

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
DNA_polymerase_beta_polypeptide: MSKRKAPQETLNGGITDMLV ELANFEKNVSQAIHKYNAYR KAASVIAKYPHKIKSGAEAK KLPGVGTKIAEKIDEFLATG KLRKLEKIRQDDTSSSINFL TRVTGIGPSAARKLVDEGIK TLEDLRKNEDKLNHHQRIGL KYFEDFEKRIPREEMLQMQD IVLNEVKKLDPEYIATVCGS FRRGAESSGDMDVLLTHPNF TSESSKQPKLLHRVVEQLQK VRFITDTLSKGETKFMGVCQ LPSENDENEYPHRRIDIRLI PKDQYYAGVLYFTGSDIFNK NMRAHALEKGFTINEYTIRP LGVTGVAGEPLPVDSEQDIF DYIQWRYREPKDRSE
1-nucleotide_gapped_double_hairpin_DNA: GGCGAAGCCTGGTGCGAAGC ACC

Data sets:
Data typeCount
13C chemical shifts29
1H chemical shifts87

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA polymerase beta1
2hairpin DNA2
3metal ion3

Entities:

Entity 1, DNA polymerase beta 335 residues - Formula weight is not available

1   METSERLYSARGLYSALAPROGLNGLUTHR
2   LEUASNGLYGLYILETHRASPMETLEUVAL
3   GLULEUALAASNPHEGLULYSASNVALSER
4   GLNALAILEHISLYSTYRASNALATYRARG
5   LYSALAALASERVALILEALALYSTYRPRO
6   HISLYSILELYSSERGLYALAGLUALALYS
7   LYSLEUPROGLYVALGLYTHRLYSILEALA
8   GLULYSILEASPGLUPHELEUALATHRGLY
9   LYSLEUARGLYSLEUGLULYSILEARGGLN
10   ASPASPTHRSERSERSERILEASNPHELEU
11   THRARGVALTHRGLYILEGLYPROSERALA
12   ALAARGLYSLEUVALASPGLUGLYILELYS
13   THRLEUGLUASPLEUARGLYSASNGLUASP
14   LYSLEUASNHISHISGLNARGILEGLYLEU
15   LYSTYRPHEGLUASPPHEGLULYSARGILE
16   PROARGGLUGLUMETLEUGLNMETGLNASP
17   ILEVALLEUASNGLUVALLYSLYSLEUASP
18   PROGLUTYRILEALATHRVALCYSGLYSER
19   PHEARGARGGLYALAGLUSERSERGLYASP
20   METASPVALLEULEUTHRHISPROASNPHE
21   THRSERGLUSERSERLYSGLNPROLYSLEU
22   LEUHISARGVALVALGLUGLNLEUGLNLYS
23   VALARGPHEILETHRASPTHRLEUSERLYS
24   GLYGLUTHRLYSPHEMETGLYVALCYSGLN
25   LEUPROSERGLUASNASPGLUASNGLUTYR
26   PROHISARGARGILEASPILEARGLEUILE
27   PROLYSASPGLNTYRTYRALAGLYVALLEU
28   TYRPHETHRGLYSERASPILEPHEASNLYS
29   ASNMETARGALAHISALALEUGLULYSGLY
30   PHETHRILEASNGLUTYRTHRILEARGPRO
31   LEUGLYVALTHRGLYVALALAGLYGLUPRO
32   LEUPROVALASPSERGLUGLNASPILEPHE
33   ASPTYRILEGLNTRPARGTYRARGGLUPRO
34   LYSASPARGSERGLU

Entity 2, hairpin DNA 23 residues - Formula weight is not available

1   DGDGDCDGDADADGDCDCDT
2   DGDGDTDGDCDGDADADGDC
3   DADCDC

Entity 3, metal ion - Mg - 24.305 Da.

1   MG

Samples:

sample_1: DNA polymerase beta polypeptide, Ile CD1-[13CH3],Leu,Val-[13CH3,12CD3][U-13C; U-15N; U-2H], 400 uM; potassium phosphate 100 mM; DTT 1 mM; sodium azide 10 mM; DSS 50 uM; 1-nucleotide gapped double hairpin DNA 450 uM; MgCl2 5 mM

sample_2: DNA polymerase beta polypeptide, Ile CD1-[13CH3],Met-[13CH3],[U-15N; U-2H], 150 uM; potassium chloride 150 mM; TRIS, [U-100% 2H], 50 mM; CDTA 1 mM; DTT 1 mM; AEBSF protease inhibitor 0.1 mM; sodium azide 0.04%; DSS 50 uM; 1-nucleotide gapped double hairpin DNA 165 uM; MgCl2 5 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.7; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 150 mM; pH: 7.6; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HMQC methylsample_1isotropicsample_conditions_1
2D 1H-13C HMQC methylsample_1isotropicsample_conditions_1
2D 1H-13C-HMQC methylsample_2isotropicsample_conditions_2
2D 1H-13C-HMQC methylsample_2isotropicsample_conditions_2
3D (HM)CM(CGCBCA)NHsample_1isotropicsample_conditions_1
3D HM(CMCGCBCA)NHsample_1isotropicsample_conditions_1
3D HMCM[CG]CBCAsample_1isotropicsample_conditions_1
3D HMCM(CGCBCA)COsample_1isotropicsample_conditions_1

Software:

VNMRJ v4.2/2.2, Agilent/Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRViewJ, Johnson, One Moon Scientific - chemical shift assignment

NMR spectrometers:

  • Agilent DD2 800 MHz
  • Agilent DD2 600 MHz
  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz

Related Database Links: