BMRB Entry 5627

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR5627

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Title:
1H, 15N, 13C Resonance Assignments of the LpxC Deacetylase from Aquifex aeolicus in Complex with the Substrate-Analog Inhibitor TU-514
Deposition date:
2002-12-17
Original release date:
2003-09-05
Authors:
Coggins, Brian; Li, Xuechen; Hindsgaul, Ole; Raetz, Christian; Zhou, Pei
Citation:

Citation: Coggins, Brian; Li, Xuechen; McClerren, Amanda; Hindsgaul, Ole; Raetz, Christian; Zhou, Pei. "Structure of the LpxC Deacetylase with a Bound Substrate-analog Inhibitor"  Nat. Struct. Biol. 10, 645-651 (2003).
PubMed: 12833153

Assembly members:

Assembly members:
UDP-3-O-acyl-GlcNAc deacetylase, polymer, 282 residues, 32145 Da.
ZN, non-polymer, 65.409 Da.
TUX, non-polymer, 431.563 Da.

Natural source:

Natural source:   Common Name: Aquifex aeolicus   Taxonomy ID: 63363   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Aquifex aeolicus

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
UDP-3-O-acyl-GlcNAc deacetylase: MGLEKTVKEKLSFEGVGIHT GEYSKLIIHPEKEGTGIRFF KNGVYIPARHEFVVHTNHST DLGFKGQRIKTVEHILSVLH LLEITNVTIEVIGNEIPILD GSGWEFYEAIRKNILNQNRE IDYFVVEEPIIVEDEGRLIK AEPSDTLEVTYEGEFKNFLG RQKFTFVEGNEEEIVLARTF CFDWEIEHIKKVGLGKGGSL KNTLVLGKDKVYNPEGLRYE NEPVRHKVFDLIGDLYLLGS PVKGKFYSFRGGHSLNVKLV KELAKKQKLTRDLPHLPSVQ AL

Data sets:
Data typeCount
1H chemical shifts1889
13C chemical shifts902
15N chemical shifts266

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1A. aeolicus LpxC1
2TU-5143
3Zinc ion2

Entities:

Entity 1, A. aeolicus LpxC 282 residues - 32145 Da.

1   METGLYLEUGLULYSTHRVALLYSGLULYS
2   LEUSERPHEGLUGLYVALGLYILEHISTHR
3   GLYGLUTYRSERLYSLEUILEILEHISPRO
4   GLULYSGLUGLYTHRGLYILEARGPHEPHE
5   LYSASNGLYVALTYRILEPROALAARGHIS
6   GLUPHEVALVALHISTHRASNHISSERTHR
7   ASPLEUGLYPHELYSGLYGLNARGILELYS
8   THRVALGLUHISILELEUSERVALLEUHIS
9   LEULEUGLUILETHRASNVALTHRILEGLU
10   VALILEGLYASNGLUILEPROILELEUASP
11   GLYSERGLYTRPGLUPHETYRGLUALAILE
12   ARGLYSASNILELEUASNGLNASNARGGLU
13   ILEASPTYRPHEVALVALGLUGLUPROILE
14   ILEVALGLUASPGLUGLYARGLEUILELYS
15   ALAGLUPROSERASPTHRLEUGLUVALTHR
16   TYRGLUGLYGLUPHELYSASNPHELEUGLY
17   ARGGLNLYSPHETHRPHEVALGLUGLYASN
18   GLUGLUGLUILEVALLEUALAARGTHRPHE
19   CYSPHEASPTRPGLUILEGLUHISILELYS
20   LYSVALGLYLEUGLYLYSGLYGLYSERLEU
21   LYSASNTHRLEUVALLEUGLYLYSASPLYS
22   VALTYRASNPROGLUGLYLEUARGTYRGLU
23   ASNGLUPROVALARGHISLYSVALPHEASP
24   LEUILEGLYASPLEUTYRLEULEUGLYSER
25   PROVALLYSGLYLYSPHETYRSERPHEARG
26   GLYGLYHISSERLEUASNVALLYSLEUVAL
27   LYSGLULEUALALYSLYSGLNLYSLEUTHR
28   ARGASPLEUPROHISLEUPROSERVALGLN
29   ALALEU

Entity 3, TU-514 - C22 H41 N O7 - 431.563 Da.

1   TUX

Entity 2, Zinc ion - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: UDP-3-O-acyl-GlcNAc deacetylase, [U-13C; U-15N], 0.3 – 0.5 mM; 3,6-anhydro-3-deoxy-N-hydroxy-3-C-hydroxymethyl-4-O-myristoyl-D-gluco-heptonamide0.33 – 0.55 mM; sodium phosphate 25 mM; potassium chloride 150 mM; dithiothreitol 4 mM; deuterium oxide, [U-2H], 5%; dimethyl sulfoxide 5%

sample_2: UDP-3-O-acyl-GlcNAc deacetylase, [U-2H; U-13C; U-15N], 0.3 – 0.5 mM; 3,6-anhydro-3-deoxy-N-hydroxy-3-C-hydroxymethyl-4-O-myristoyl-D-gluco-heptonamide0.33 – 0.55 mM; sodium phosphate 25 mM; potassium chloride 150 mM; dithiothreitol 4 mM; deuterium oxide, [U-2H], 5%; dimethyl sulfoxide 5%

Normal_conditions: pH: 6.5 na; temperature: 323 K

Experiments:

NameSampleSample stateSample conditions
1H-15N HSQCnot availablenot availableNormal_conditions
HNCAnot availablenot availableNormal_conditions
HN(CO)CAnot availablenot availableNormal_conditions
HN(CA)CBnot availablenot availableNormal_conditions
HN(COCA)CBnot availablenot availableNormal_conditions
HNCOnot availablenot availableNormal_conditions
HCCH-TOCSYnot availablenot availableNormal_conditions
H(CCO)NH-TOCSYnot availablenot availableNormal_conditions
15N NOESY-HSQCnot availablenot availableNormal_conditions
13C NOESY-HSQCnot availablenot availableNormal_conditions
H(CCO)NHnot availablenot availableNormal_conditions

Software:

FELIX v2000 - data processing

XEASY v1.3.30 - spectrum analysis

PACES v1.0 - sequential assignment

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian INOVA 800 MHz

Related Database Links:

BMRB 17416
PDB
GB AAC07605
REF NP_214214 WP_010881151
SP O67648
AlphaFold O67648

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