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BMRB: 30943


30943
7RY6
Solution structure of first cyclization domain (Cy1) from yersiniabactin synthetase
Authors
Mishra, S.H., Frueh, D.P.
Assembly
HMWP2 nonribosomal peptide synthetase (E.C.6.3.2.-)
Entity
1. HMWP2 nonribosomal peptide synthetase (E.C.6.3.2.-) (polymer), 453 monomers, 51852.09 Da Detail

MPDESSWPNM TESTPFPLTP VQHAYLTGRM PGQTLGGVGC HLYQEFEGHC LTASQLEQAI TTLLQRHPML HIAFRPDGQQ VWLPQPYWNG VTVHDLRHND AESRQAYLDA LRQRLSHRLL RVEIGETFDF QLTLLPDNRH RLHVNIDLLI MDASSFTLFF DELNALLAGE SLPAIDTRYD FRSYLLHQQK INQPLRDDAR AYWLAKASTL PPAPVLPLAC EPATLREVRN TRRRMIVPAT RWHAFSNRAG EYGVTPTMAL ATCFSAVLAR WGGLTRLLLN ITLFDRQPLH PAVGAMLADF TNILLLDTAC DGDTVSNLAR KNQLTFTEDW EHRHWSGVEL LRELKRQQRY PHGAPVVFTS NLGRSLYSSR AESPLGEPEW GISQTPQVWI DHLAFEHHGE VWLQWDSNDA LFPPALVETL FDAYCQLINQ LCDDESAWQK PFADMLEHHH HHH


Formula weight
51852.09 Da
Source organism
Yersinia pestis
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 94.5 %, Completeness: 53.3 %, Completeness (bb): 90.5 % Detail
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Polymer type: polypeptide(L)

Total1H13C15N
All53.3 % (2859 of 5361)37.7 % (1038 of 2756)68.0 % (1425 of 2096)77.8 % (396 of 509)
Backbone90.5 % (2405 of 2658)86.6 % (778 of 898)93.0 % (1243 of 1337)90.8 % (384 of 423)
Sidechain27.2 % (852 of 3134)14.0 % (260 of 1858)48.7 % (580 of 1190)14.0 % (12 of 86)
Aromatic 9.0 % (48 of 534)12.0 % (32 of 267) 1.6 % (4 of 254)92.3 % (12 of 13)
Methyl73.8 % (384 of 520)66.9 % (174 of 260)80.8 % (210 of 260)

1. entity 1

MPDESSWPNM TESTPFPLTP VQHAYLTGRM PGQTLGGVGC HLYQEFEGHC LTASQLEQAI TTLLQRHPML HIAFRPDGQQ VWLPQPYWNG VTVHDLRHND AESRQAYLDA LRQRLSHRLL RVEIGETFDF QLTLLPDNRH RLHVNIDLLI MDASSFTLFF DELNALLAGE SLPAIDTRYD FRSYLLHQQK INQPLRDDAR AYWLAKASTL PPAPVLPLAC EPATLREVRN TRRRMIVPAT RWHAFSNRAG EYGVTPTMAL ATCFSAVLAR WGGLTRLLLN ITLFDRQPLH PAVGAMLADF TNILLLDTAC DGDTVSNLAR KNQLTFTEDW EHRHWSGVEL LRELKRQQRY PHGAPVVFTS NLGRSLYSSR AESPLGEPEW GISQTPQVWI DHLAFEHHGE VWLQWDSNDA LFPPALVETL FDAYCQLINQ LCDDESAWQK PFADMLEHHH HHH

Show sample condition
Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 588 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
1Cy1[U-100% 13C; U-100% 15N; U-100% 2H]588 uM
2sodium phosphatenatural abundance20 mM
3sodium chloridenatural abundance10 mM
4EDTAnatural abundance1 mM
5DTTnatural abundance5 mM
6DSSnatural abundance0.25 mM
Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 429 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 12 mg/mL Pf1 phage, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
7Cy1[U-100% 13C; U-100% 15N; U-100% 2H]429 uM
8sodium phosphatenatural abundance20 mM
9sodium chloridenatural abundance10 mM
10EDTAnatural abundance1 mM
11DTTnatural abundance5 mM
12DSSnatural abundance0.25 mM
13Pf1 phagenatural abundance12 mg/mL
Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
14Cy1[U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (D1)]586 uM
15sodium phosphatenatural abundance20 mM
16sodium chloridenatural abundance10 mM
17EDTAnatural abundance1 mM
18DTTnatural abundance5 mM
19DSSnatural abundance0.25 mM
Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 600 uM U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu delta-2, Val gamma-2, and Ile delta1 Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.03 % w/v Sodium Azide, 0.25 mM DSS, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
20Cy1[U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu D2, Val G2, and Ile D1]600 uM
21sodium phosphatenatural abundance20 mM
22sodium chloridenatural abundance10 mM
23EDTAnatural abundance1 mM
24DTTnatural abundance5 mM
25DSSnatural abundance0.25 mM
26Sodium Azidenatural abundance0.03 % w/v
Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 986 uM U-100% 13C, U-100% 15N; U-70% 2H; Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
27Cy1[U-100% 13C, U-100% 15N; U-70% 2H]986 uM
28sodium phosphatenatural abundance20 mM
29sodium chloridenatural abundance10 mM
30EDTAnatural abundance1 mM
31DTTnatural abundance5 mM
32DSSnatural abundance0.25 mM
Sample #6

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 350 uM U-100% 2H, U-100% 15N; 1H and 15N for Phe and Tyr; 1H and 13C for methyls of Ile (delta-1), Leu (delta-1 and delta-2), and Val (gamma-1 and gamma-2) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
33Cy1[U-100% 2H, U-100% 15N; 1H and 15N for Phe and Tyr; 1H and 13C for methyls of Ile (D1), Leu (D1 and D2), and Val (G1 and G2)]350 uM
34sodium phosphatenatural abundance20 mM
35sodium chloridenatural abundance10 mM
36EDTAnatural abundance1 mM
37DTTnatural abundance5 mM
38DSSnatural abundance0.25 mM

Release date
2021-09-01
Citation
Global protein dynamics as communication sensors in peptide synthetase domains
Mishra, S.H., Kancherla, A.K., Marincin, K.A., Bouvignies, G., Nerli, S., Sgourakis, N., Dowling, D.P., Frueh, D.P.
Sci. Adv. (2022), 8, eabn6549-eabn6549, PubMed 35857508 , DOI 10.1126/sciadv.abn6549 ,
Entries sharing articles BMRB: 1 entries Detail
  BMRB: 51105 released on 2021-09-26
    Title Ybt Cy1 D391N
Related entities 1. HMWP2 nonribosomal peptide synthetase (E.C.6.3.2.-), : 1 : 35 entities Detail
More details for 36 related entities
Experiments performed 34 experiments Detail
nullKeywords Heterocyclization, LIGASE, Nonribosomal Peptide Synthetase, Peptide Bond Formation