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BMRB: 30820


30820
7KW9
NMR Structure of a tRNA 2'-phosphotransferase from Runella slithyformis in complex with NAD+
Authors
Alphonse, S., Dantuluri, S., Banerjee, A., Shuman, S., Ghose, R.
Assembly
tRNA 2'-phosphotransferase (E.C.2.7.1.160)
Entity
1. tRNA 2'-phosphotransferase (E.C.2.7.1.160), entity 1 (polymer, Thiol state: not present), 178 monomers, 19810.75 Da Detail

GSHMVKVSKF LSLVLRHNPA LIGLDLDANG WAPVKELLAK MKAKGHGISM EELKHIVETN SKKRFAFSEN FEKIRANQGH SVEVDLGYEK QVPPAVLFHG TAEKNFDLIL KDGIKKMSRH HVHLSQDITT ARKVGMRHGK PVVLSVDAKG MADGGFDFYL SNNGVWLIDF VPAEFIKV


2. tRNA 2'-phosphotransferase (E.C.2.7.1.160), entity NAD (non-polymer), 663.425 Da
Total weight
20474.176 Da
Max. entity weight
19810.75 Da
Source organism
Runella slithyformis
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 97.2 %, Completeness: 83.2 %, Completeness (bb): 89.3 % Detail
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Polymer type: polypeptide(L)

Total1H13C15N
All83.2 % (1762 of 2117)81.1 % (890 of 1097)84.2 % (698 of 829)91.1 % (174 of 191)
Backbone89.3 % (943 of 1056)90.4 % (330 of 365)87.1 % (452 of 519)93.6 % (161 of 172)
Sidechain78.3 % (959 of 1224)76.5 % (560 of 732)81.6 % (386 of 473)68.4 % (13 of 19)
Aromatic58.9 % (106 of 180)63.3 % (57 of 90)53.4 % (47 of 88)100.0 % (2 of 2)
Methyl99.0 % (204 of 206)99.0 % (102 of 103)99.0 % (102 of 103)

1. entity 1

GSHMVKVSKF LSLVLRHNPA LIGLDLDANG WAPVKELLAK MKAKGHGISM EELKHIVETN SKKRFAFSEN FEKIRANQGH SVEVDLGYEK QVPPAVLFHG TAEKNFDLIL KDGIKKMSRH HVHLSQDITT ARKVGMRHGK PVVLSVDAKG MADGGFDFYL SNNGVWLIDF VPAEFIKV

Show sample condition
Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 290.15 K, pH 7, Details 600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
1Tpt1[U-13C; U-15N]600 uM
2NICOTINAMIDE-ADENINE-DINUCLEOTIDEnatural abundance2.4 mM
3HEPESnatural abundance20 mM
4sodium chloridenatural abundance200 mM
5DTTnatural abundance2 mM
6EDTA[U-2H]2 mM
7glycerol[U-2H]5 % v/v
8AEBSF protease inhibitornatural abundance1 mM
9sodium azidenatural abundance0.04 % w/v
10DSSnatural abundance50 uM
Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 290.15 K, pH 7, Details 280 uM [U-13C; U-15N] Tpt1, 1.12 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
11Tpt1[U-13C; U-15N]280 uM
12NICOTINAMIDE-ADENINE-DINUCLEOTIDEnatural abundance1.12 mM
13HEPESnatural abundance20 mM
14sodium chloridenatural abundance200 mM
15DTTnatural abundance2 mM
16EDTA[U-2H]2 mM
17glycerol[U-2H]5 % v/v
18AEBSF protease inhibitornatural abundance1 mM
19sodium azidenatural abundance0.04 % w/v
20DSSnatural abundance50 uM
Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 290.15 K, pH 7, Details 325 uM [U-13C; U-15N] Tpt1, 1.3 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS, 100% D2O


#NameIsotope labelingTypeConcentration
21Tpt1[U-13C; U-15N]325 uM
22NICOTINAMIDE-ADENINE-DINUCLEOTIDEnatural abundance1.3 mM
23HEPESnatural abundance20 mM
24sodium chloridenatural abundance200 mM
25DTTnatural abundance2 mM
26EDTA[U-2H]2 mM
27glycerol[U-2H]5 % v/v
28AEBSF protease inhibitornatural abundance1 mM
29sodium azidenatural abundance0.04 % w/v
30DSSnatural abundance50 uM
Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 290.15 K, pH 7, Details 300 uM [U-13C; U-15N] Tpt1, 1.2 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS, 100% D2O


#NameIsotope labelingTypeConcentration
31Tpt1[U-13C; U-15N]300 uM
32NICOTINAMIDE-ADENINE-DINUCLEOTIDEnatural abundance1.2 mM
33HEPESnatural abundance20 mM
34sodium chloridenatural abundance200 mM
35DTTnatural abundance2 mM
36EDTA[U-2H]2 mM
37glycerol[U-2H]5 % v/v
38AEBSF protease inhibitornatural abundance1 mM
39sodium azidenatural abundance0.04 % w/v
40DSSnatural abundance50 uM
Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 290.15 K, pH 7, Details 500 uM [U-13C; U-15N; U-2H] Tpt1, 2 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
41Tpt1[U-13C; U-15N; U-2H]500 uM
42NICOTINAMIDE-ADENINE-DINUCLEOTIDEnatural abundance2 mM
43HEPESnatural abundance20 mM
44sodium chloridenatural abundance200 mM
45DTTnatural abundance2 mM
46EDTA[U-2H]2 mM
47glycerol[U-2H]5 % v/v
48AEBSF protease inhibitornatural abundance1 mM
49sodium azidenatural abundance0.04 % w/v
50DSSnatural abundance50 uM
Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 290.15 K, pH 7, Details 400 uM [U-13C; U-15N] Tpt1, 1.6 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS, 100% D2O


#NameIsotope labelingTypeConcentration
51Tpt1[U-13C; U-15N]400 uM
52NICOTINAMIDE-ADENINE-DINUCLEOTIDEnatural abundance1.6 mM
53HEPESnatural abundance20 mM
54sodium chloridenatural abundance200 mM
55DTTnatural abundance2 mM
56EDTA[U-2H]2 mM
57glycerol[U-2H]5 % v/v
58AEBSF protease inhibitornatural abundance1 mM
59sodium azidenatural abundance0.04 % w/v
60DSSnatural abundance50 uM

Release date
2021-01-03
Citation
NMR solution structures of Runella slithyformis RNA 2'-phosphotransferase Tpt1 provide insights into NAD+ binding and specificity
Alphonse, S., Banerjee, A., Dantuluri, S., Shuman, S., Ghose, R.
Nucleic Acids Res. (2021), 49, 9607-9624, PubMed 33880546 , DOI 10.1093/nar/gkab241 ,
Related entities 1. tRNA 2'-phosphotransferase (E.C.2.7.1.160), entity 1, : 1 : 1 : 95 entities Detail
More details for 97 related entities
Experiments performed 20 experiments Detail
Chemical shift validation 4 contents Detail
Keywords TRANSFERASE, tRNA 2'-phosphotransferase NAD+