BMRB Entry 27560

Title:
protein-gapped DNA complex (Polymerase beta) ILV Methyl Assignments
Deposition date:
2018-07-25
Original release date:
2018-11-15
Authors:
Liptak, Cary; Mahmoud, Mariam; Eckenroth, Brian; Moreno, Marcus; East, Kyle; Alnajjar, Khadijeh; Huang, Ji; Towle-Weicksel, Jamie; Doubli, Sylvie; Loria, J Patrick; Sweasy, Joann
Citation:

Citation: Liptak, Cary; Mahmoud, Mariam; Eckenroth, Brian; Moreno, Marcus; East, Kyle; Alnajjar, Khadijeh; Huang, Ji; Towle-Weicksel, Jamie; Doubli, Sylvie; Loria, J Patrick; Sweasy, Joann. "I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity"  Nucleic Acids Res. 46, 10740-10756 (2018).
PubMed: 30239932

Assembly members:

Assembly members:
DNA_Polymerase_beta, polymer, 335 residues, Formula weight is not available
gapped_DNA_template, polymer, 20 residues, Formula weight is not available
gapped_DNA_upstream, polymer, 11 residues, Formula weight is not available
gapped_DNA_downstream, polymer, 8 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source:   Production method: purified from the natural source   Host organism: Escherichia coli   Vector: pET43.1b

Data sets:
Data typeCount
13C chemical shifts76
1H chemical shifts228

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1chain A1
2template2
3upstream3
4downstream4

Entities:

Entity 1, chain A 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, template 20 residues - Formula weight is not available

1   DCDGDADCDCDGDADCDGDG
2   DCDGDCDADTDCDADGDCDC

Entity 3, upstream 11 residues - Formula weight is not available

1   DGDGDCDTDGDADTDGDCDG
2   DC

Entity 4, downstream 8 residues - Formula weight is not available

1   DGDTDCDGDGDTDCDG

Samples:

sample_1: DNA Polymerase beta, [U-13C; U-15N; U-2H; 99.5% 1HD-Ile,Leu; 99.5% 1HG-Val], 430 uM; potassium chloride 100 mM; HEPES 50 mM; DTT 2 mM; magnesium chloride 10 mM; gapped DNA template 720 mM; gapped DNA upstream 720 mM; gapped DNA downstream 720 mM

sample_conditions_1: pH: 7.36; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQC methylsample_1isotropicsample_conditions_1
HMCM[CG]CBCAsample_1isotropicsample_conditions_1
HMCM[CGCBCA]COsample_1isotropicsample_conditions_1
HMCM[CBCA]COsample_1isotropicsample_conditions_1
Methyl-Methyl HMQC-NOESY-HMQCsample_1isotropicsample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

  • Varian DD2 800 MHz
  • Varian INOVA 600 MHz

Related Database Links:

SP P06766 Q8K409
AlphaFold Q4G081 Q922Z7