BMRB Entry 52158

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52158

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Title:
NMR analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria
Deposition date:
2023-10-01
Original release date:
2023-10-09
Authors:
Konuma, Tsuyoshi; Takai, Tomoyo; Tsuchiya, Chieko; Nishida, Masayuki; Hashiba, Miyu; Yamada, Yudai; Shirai, Haruka; Oe, Ayaka; Nagadoi, Aritaka; Chikaishi, Eriko; Akagi, Ken-ichi; Akashi, Satoko; Yamazaki, Toshio; Akutsu, Hideo; Ikegami, Takahisa
Citation:

Citation: Konuma, Tsuyoshi; Takai, Tomoyo; Tsuchiya, Chieko; Nishida, Masayuki; Hashiba, Miyu; Yamada, Yudai; Shirai, Haruka; Oe, Ayaka; Nagadoi, Aritaka; Chikaishi, Eriko; Akagi, Ken-ichi; Akashi, Satoko; Yamazaki, Toshio; Akutsu, Hideo; Ikegami, Takahisa. "Analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria"  Protein Sci. 33, e5002-e5002 (2024).
PubMed: 38723146

Assembly members:

Assembly members:
entity_1, polymer, 210 residues, Formula weight is not available
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Enterococcus faecalis   Taxonomy ID: 1351   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Enterococcus faecalis

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-47b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPGMGGSGMEIGFTFLDEIV HGVRWDAKYATWDNFTGKPV DGYEVNRIVGTYELAESLLK AKELAATQGYGLLLWDGYRP KRAVNSFMQWAAQPENNLTK ESYYPNIDRTEMISKGYVAS KSSHSRGSAIDLTLYRLDTG ELVPMGSRFDFMDERSHHAA NGISSNEAQNRRRLRSIMEN SGFEAYSLEWWHYVLRDEPY PNSYFDFPVK

Data sets:
Data typeCount
13C chemical shifts1171
15N chemical shifts383
1H chemical shifts381

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1VanX, chain 11
2VanX, chain 21
3Zn2+, 12
4Zn2+, 22

Entities:

Entity 1, VanX, chain 1 210 residues - Formula weight is not available

The sequence GPGMGGSG corresponds to the peptide that remains in the N-terminus after cleavage of the (His)6 tag with HRV3C. The residual number 1 starts with the Met in the subsequent sequence MEIGF.

1   GLYPROGLYMETGLYGLYSERGLYMETGLU
2   ILEGLYPHETHRPHELEUASPGLUILEVAL
3   HISGLYVALARGTRPASPALALYSTYRALA
4   THRTRPASPASNPHETHRGLYLYSPROVAL
5   ASPGLYTYRGLUVALASNARGILEVALGLY
6   THRTYRGLULEUALAGLUSERLEULEULYS
7   ALALYSGLULEUALAALATHRGLNGLYTYR
8   GLYLEULEULEUTRPASPGLYTYRARGPRO
9   LYSARGALAVALASNSERPHEMETGLNTRP
10   ALAALAGLNPROGLUASNASNLEUTHRLYS
11   GLUSERTYRTYRPROASNILEASPARGTHR
12   GLUMETILESERLYSGLYTYRVALALASER
13   LYSSERSERHISSERARGGLYSERALAILE
14   ASPLEUTHRLEUTYRARGLEUASPTHRGLY
15   GLULEUVALPROMETGLYSERARGPHEASP
16   PHEMETASPGLUARGSERHISHISALAALA
17   ASNGLYILESERSERASNGLUALAGLNASN
18   ARGARGARGLEUARGSERILEMETGLUASN
19   SERGLYPHEGLUALATYRSERLEUGLUTRP
20   TRPHISTYRVALLEUARGASPGLUPROTYR
21   PROASNSERTYRPHEASPPHEPROVALLYS

Entity 2, Zn2+, 1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: D-alanyl-D-alanine dipeptidase, VanX, [U-13C; U-15N; U-2H], 0.125 mM; ZnCl2 30 uM; potassium phosphate 50 mM

sample_2: D-alanyl-D-alanine dipeptidase, VanX, [U-13C; U-15N; U-2H], 0.125 mM; ZnCl2 30 uM; sodium acetate 20 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 20 mM; pH: 4; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
2D 1H-15N TROSYsample_2isotropicsample_conditions_2

Software:

NMRFAM-SPARKY - chemical shift assignment

NMR spectrometers:

  • Bruker AVANCE III 800 MHz

Related Database Links:

UNP A0A286KC57_ENTAV

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks