BMRB Entry 52158

Name: NMR analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria
Published: 2023-10-09

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

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	1171
15N chemical shifts	383
1H chemical shifts	381

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	VanX, chain 1	1
2	VanX, chain 2	1
3	Zn2+, 1	2
4	Zn2+, 2	2

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	GLY	PRO	GLY	MET	GLY	GLY	SER	GLY	MET	GLU
2	ILE	GLY	PHE	THR	PHE	LEU	ASP	GLU	ILE	VAL
3	HIS	GLY	VAL	ARG	TRP	ASP	ALA	LYS	TYR	ALA
4	THR	TRP	ASP	ASN	PHE	THR	GLY	LYS	PRO	VAL
5	ASP	GLY	TYR	GLU	VAL	ASN	ARG	ILE	VAL	GLY
6	THR	TYR	GLU	LEU	ALA	GLU	SER	LEU	LEU	LYS
7	ALA	LYS	GLU	LEU	ALA	ALA	THR	GLN	GLY	TYR
8	GLY	LEU	LEU	LEU	TRP	ASP	GLY	TYR	ARG	PRO
9	LYS	ARG	ALA	VAL	ASN	SER	PHE	MET	GLN	TRP
10	ALA	ALA	GLN	PRO	GLU	ASN	ASN	LEU	THR	LYS
11	GLU	SER	TYR	TYR	PRO	ASN	ILE	ASP	ARG	THR
12	GLU	MET	ILE	SER	LYS	GLY	TYR	VAL	ALA	SER
13	LYS	SER	SER	HIS	SER	ARG	GLY	SER	ALA	ILE
14	ASP	LEU	THR	LEU	TYR	ARG	LEU	ASP	THR	GLY
15	GLU	LEU	VAL	PRO	MET	GLY	SER	ARG	PHE	ASP
16	PHE	MET	ASP	GLU	ARG	SER	HIS	HIS	ALA	ALA
17	ASN	GLY	ILE	SER	SER	ASN	GLU	ALA	GLN	ASN
18	ARG	ARG	ARG	LEU	ARG	SER	ILE	MET	GLU	ASN
19	SER	GLY	PHE	GLU	ALA	TYR	SER	LEU	GLU	TRP
20	TRP	HIS	TYR	VAL	LEU	ARG	ASP	GLU	PRO	TYR
21	PRO	ASN	SER	TYR	PHE	ASP	PHE	PRO	VAL	LYS

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

1

ZN

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_2	isotropic	sample_conditions_2

BMRB Entry 52158

Additional metadata:

Assembly:

Entities:

Samples:

Experiments:

Software:

NMR spectrometers:

Related Database Links:

1	GLY	PRO	GLY	MET	GLY	GLY	SER	GLY	MET	GLU
2	ILE	GLY	PHE	THR	PHE	LEU	ASP	GLU	ILE	VAL
3	HIS	GLY	VAL	ARG	TRP	ASP	ALA	LYS	TYR	ALA
4	THR	TRP	ASP	ASN	PHE	THR	GLY	LYS	PRO	VAL
5	ASP	GLY	TYR	GLU	VAL	ASN	ARG	ILE	VAL	GLY
6	THR	TYR	GLU	LEU	ALA	GLU	SER	LEU	LEU	LYS
7	ALA	LYS	GLU	LEU	ALA	ALA	THR	GLN	GLY	TYR
8	GLY	LEU	LEU	LEU	TRP	ASP	GLY	TYR	ARG	PRO
9	LYS	ARG	ALA	VAL	ASN	SER	PHE	MET	GLN	TRP
10	ALA	ALA	GLN	PRO	GLU	ASN	ASN	LEU	THR	LYS
11	GLU	SER	TYR	TYR	PRO	ASN	ILE	ASP	ARG	THR
12	GLU	MET	ILE	SER	LYS	GLY	TYR	VAL	ALA	SER
13	LYS	SER	SER	HIS	SER	ARG	GLY	SER	ALA	ILE
14	ASP	LEU	THR	LEU	TYR	ARG	LEU	ASP	THR	GLY
15	GLU	LEU	VAL	PRO	MET	GLY	SER	ARG	PHE	ASP
16	PHE	MET	ASP	GLU	ARG	SER	HIS	HIS	ALA	ALA
17	ASN	GLY	ILE	SER	SER	ASN	GLU	ALA	GLN	ASN
18	ARG	ARG	ARG	LEU	ARG	SER	ILE	MET	GLU	ASN
19	SER	GLY	PHE	GLU	ALA	TYR	SER	LEU	GLU	TRP
20	TRP	HIS	TYR	VAL	LEU	ARG	ASP	GLU	PRO	TYR
21	PRO	ASN	SER	TYR	PHE	ASP	PHE	PRO	VAL	LYS

1	GLY	PRO	GLY	MET	GLY	GLY	SER	GLY	MET	GLU
2	ILE	GLY	PHE	THR	PHE	LEU	ASP	GLU	ILE	VAL
3	HIS	GLY	VAL	ARG	TRP	ASP	ALA	LYS	TYR	ALA
4	THR	TRP	ASP	ASN	PHE	THR	GLY	LYS	PRO	VAL
5	ASP	GLY	TYR	GLU	VAL	ASN	ARG	ILE	VAL	GLY
6	THR	TYR	GLU	LEU	ALA	GLU	SER	LEU	LEU	LYS
7	ALA	LYS	GLU	LEU	ALA	ALA	THR	GLN	GLY	TYR
8	GLY	LEU	LEU	LEU	TRP	ASP	GLY	TYR	ARG	PRO
9	LYS	ARG	ALA	VAL	ASN	SER	PHE	MET	GLN	TRP
10	ALA	ALA	GLN	PRO	GLU	ASN	ASN	LEU	THR	LYS
11	GLU	SER	TYR	TYR	PRO	ASN	ILE	ASP	ARG	THR
12	GLU	MET	ILE	SER	LYS	GLY	TYR	VAL	ALA	SER
13	LYS	SER	SER	HIS	SER	ARG	GLY	SER	ALA	ILE
14	ASP	LEU	THR	LEU	TYR	ARG	LEU	ASP	THR	GLY
15	GLU	LEU	VAL	PRO	MET	GLY	SER	ARG	PHE	ASP
16	PHE	MET	ASP	GLU	ARG	SER	HIS	HIS	ALA	ALA
17	ASN	GLY	ILE	SER	SER	ASN	GLU	ALA	GLN	ASN
18	ARG	ARG	ARG	LEU	ARG	SER	ILE	MET	GLU	ASN
19	SER	GLY	PHE	GLU	ALA	TYR	SER	LEU	GLU	TRP
20	TRP	HIS	TYR	VAL	LEU	ARG	ASP	GLU	PRO	TYR
21	PRO	ASN	SER	TYR	PHE	ASP	PHE	PRO	VAL	LYS

1	GLY	PRO	GLY	MET	GLY	GLY	SER	GLY	MET	GLU
2	ILE	GLY	PHE	THR	PHE	LEU	ASP	GLU	ILE	VAL
3	HIS	GLY	VAL	ARG	TRP	ASP	ALA	LYS	TYR	ALA
4	THR	TRP	ASP	ASN	PHE	THR	GLY	LYS	PRO	VAL
5	ASP	GLY	TYR	GLU	VAL	ASN	ARG	ILE	VAL	GLY
6	THR	TYR	GLU	LEU	ALA	GLU	SER	LEU	LEU	LYS
7	ALA	LYS	GLU	LEU	ALA	ALA	THR	GLN	GLY	TYR
8	GLY	LEU	LEU	LEU	TRP	ASP	GLY	TYR	ARG	PRO
9	LYS	ARG	ALA	VAL	ASN	SER	PHE	MET	GLN	TRP
10	ALA	ALA	GLN	PRO	GLU	ASN	ASN	LEU	THR	LYS
11	GLU	SER	TYR	TYR	PRO	ASN	ILE	ASP	ARG	THR
12	GLU	MET	ILE	SER	LYS	GLY	TYR	VAL	ALA	SER
13	LYS	SER	SER	HIS	SER	ARG	GLY	SER	ALA	ILE
14	ASP	LEU	THR	LEU	TYR	ARG	LEU	ASP	THR	GLY
15	GLU	LEU	VAL	PRO	MET	GLY	SER	ARG	PHE	ASP
16	PHE	MET	ASP	GLU	ARG	SER	HIS	HIS	ALA	ALA
17	ASN	GLY	ILE	SER	SER	ASN	GLU	ALA	GLN	ASN
18	ARG	ARG	ARG	LEU	ARG	SER	ILE	MET	GLU	ASN
19	SER	GLY	PHE	GLU	ALA	TYR	SER	LEU	GLU	TRP
20	TRP	HIS	TYR	VAL	LEU	ARG	ASP	GLU	PRO	TYR
21	PRO	ASN	SER	TYR	PHE	ASP	PHE	PRO	VAL	LYS