BMRB Entry 19760

Name: PlpA plays a central role in lipid homeostasis in Gram-negative bacterial outer membranes
Published: 2022-06-10

Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19760

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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:

PlpA plays a central role in lipid homeostasis in Gram-negative bacterial outer membranes

Deposition date:

2014-02-03

Original release date:

2022-06-10

Authors:

Morris, Faye; Knowles, Timothy; Maderbocus, Riyaz; Jeeves, Mark; Kirwan, Jennifer; Heinz, Eva; Wells, Timothy; Browning, Douglas; Sevastsyanovich, Yanina; Leyton, Denisse; Rossiter, Amanda; Bavro, Vassiliy; Sridhar, Pooja; Ward, Douglas; Shimwell, Neil; Martin, Ashley; Sahl, Jason; Wardius, Catherine; Walker, Daniel; Lithgow, Trevor; Viant, Mark; Rasko, David; Cunningham, Adam; Overduin, Michael; Henderson, Ian

Citation:

Citation: Bryant, Jack Alfred; Morris, Faye; Knowles, Timothy; Maderbocus, Riyaz; Heinz, Eva; Boelter, Gabriela; Alodaini, Dema; Colyer, Adam; Wotherspoon, Peter; Staunton, Kara; Jeeves, Mark; Browning, Douglas; Sevastsyanovich, Yanina; Wells, Timothy; Rossiter, Amanda; Bavro, Vassiliy; Sridhar, Pooja; Ward, Douglas; Chong, Zhi-Soon; Goodall, Emily Ca; Icke, Christopher; Teo, Alvin Ck; Chng, Shu-Sin; Roper, David; Lithgow, Trevor; Cunningham, Adam; Banzhaf, Manuel; Overduin, Michael; Henderson, Ian. "Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation" Elife 9, .-. (2020).
PubMed: 33315009

Assembly members:

Assembly members:
PlpA, polymer, 182 residues, 18772.311 Da.

Natural source:

Natural source: Common Name: enterobacteria Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET26b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PlpA: IAAAVVGTAAVGTKAATDPR SVGTQVDDGTLEVRVNSALS KDEQIKKEARINVTAYQGKV LLVGQSPNAELSARAKQIAM GVDGANEVYNEIRQGQPIGL GEASNDTWITTKVRSQLLTS DLVKSSNVKVTTENGEVFLM GLVTEREAKAAADIASRVSG VKRVTTAFTFIKGGLEHHHH HH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	686
15N chemical shifts	172
1H chemical shifts	1023

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1

Entities:

Entity 1, entity 182 residues - 18772.311 Da.

Residue 20 - represents non-native sequence. Replacement of Val with Ile due to cloning Residues 192-195 - Non-native due to cloning strategy Residues 196-201 - Non native - His Tag

1

ILE

ALA

VAL

GLY

THR

ALA

2

VAL

GLY

THR

LYS

ALA

THR

ASP

PRO

ARG

3

SER

VAL

GLY

THR

GLN

VAL

ASP

GLY

THR

4

LEU

GLU

VAL

ARG

VAL

ASN

SER

ALA

LEU

SER

5

LYS

ASP

GLU

GLN

ILE

LYS

GLU

ALA

ARG

6

ILE

ASN

VAL

THR

ALA

TYR

GLN

GLY

LYS

VAL

7

LEU

VAL

GLY

GLN

SER

PRO

ASN

ALA

GLU

8

LEU

SER

ALA

ARG

ALA

LYS

GLN

ILE

ALA

MET

9

GLY

VAL

ASP

GLY

ALA

ASN

GLU

VAL

TYR

ASN

10

GLU

ILE

ARG

GLN

GLY

GLN

PRO

ILE

GLY

LEU

11

GLY

GLU

ALA

SER

ASN

ASP

THR

TRP

ILE

THR

12

THR

LYS

VAL

ARG

SER

GLN

LEU

THR

SER

13

ASP

LEU

VAL

LYS

SER

ASN

VAL

LYS

VAL

14

THR

GLU

ASN

GLY

GLU

VAL

PHE

LEU

MET

15

GLY

LEU

VAL

THR

GLU

ARG

GLU

ALA

LYS

ALA

16

ALA

ASP

ILE

ALA

SER

ARG

VAL

SER

GLY

17

VAL

LYS

ARG

VAL

THR

ALA

PHE

THR

PHE

18

ILE

LYS

GLY

LEU

GLU

HIS

19

HIS

Samples:

sample_1: PlpA, [U-98% 13C; U-98% 15N], 1.5 mM; sodium phosphate 50 mM; sodium chloride 50 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.05 M; pH: 6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D H(C)CH-TOCSY	sample_1	isotropic	sample_conditions_1
3D (H)CCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY-HSQC aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY-HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY-HSQC	sample_1	isotropic	sample_conditions_1
H(C)CONH	sample_1	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

ARIA v2.3, Linge, O'Donoghue and Nilges - refinement

SPARKY, Goddard - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

ProcheckNMR, Laskowski and MacArthur - refinement

NMR spectrometers:

Varian INOVA 800 MHz

UNP	P64596
AlphaFold	Q2M960