SASDEB6: Staphylococcus aureus glucosamine-6-phosphate deaminase

Basic information

• Entry: Database: SASBDB / ID: SASDEB6

Sample

Staphylococcus aureus glucosamine-6-phosphate deaminase

• Glucosamine-6-phosphate deaminase (protein), Staphylococcus aureus (strain USA300 / TCH1516)

Function / homology

Function:

glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine metabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process

Domain/homology:

Glucosamine-6-phosphate isomerase, conserved site / Glucosamine/galactosamine-6-phosphate isomerases signature. / Glucosamine-6-phosphate isomerase / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / NagB/RpiA transferase-like

Component:

Glucosamine-6-phosphate deaminase

• Biological species: Staphylococcus aureus (strain USA300 / TCH1516) (bacteria)
• Citation: Journal: FEBS Lett / Year: 2019; Title: Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus.; Authors: James S Davies / David Coombes / Christopher R Horne / F Grant Pearce / Rosmarie Friemann / Rachel A North / Renwick C J Dobson / ; Abstract: N-Acetylglucosamine-6-phosphate deacetylase (NagA) and glucosamine-6-phosphate deaminase (NagB) are branch point enzymes that direct amino sugars into different pathways. For Staphylococcus aureus NagA, analytical ultracentrifugation and small-angle X-ray scattering data demonstrate that it is an asymmetric dimer in solution. Initial rate experiments show hysteresis, which may be related to pathway regulation, and kinetic parameters similar to other bacterial isozymes. The enzyme binds two Zn ions and is not substrate inhibited, unlike the Escherichia coli isozyme. S. aureus NagB adopts a novel dimeric structure in solution and shows kinetic parameters comparable to other Gram-positive isozymes. In summary, these functional data and solution structures are of use for understanding amino sugar metabolism in S. aureus, and will inform the design of inhibitory molecules.

Contact author

• James Davies (University of Canterbury)

Models

• Model #2492: ; Type: atomic; Comment: Dimeric structure taken from the E. coli hexameric glucosamine-6-phosphate deaminase.; Chi-square value: 0.536; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Staphylococcus aureus glucosamine-6-phosphate deaminase; Specimen concentration: 6 mg/ml
• Buffer: Name: 20 mM Tris-HCl 150 mM NaCl / pH: 8

Entity #1331

Type: protein / Description: Glucosamine-6-phosphate deaminase / Formula weight: 28.467 / Num. of mol.: 2 / Source: Staphylococcus aureus (strain USA300 / TCH1516) / References: UniProt: A8YZR7
Sequence:

MKVLNLGSKK QASFYVACEL YKEMAFNQHC KLGLATGGTM TDLYEQLVKL LNKNQLNVDN VSTFNLDEYV GLTASHPQSY HYYMDDMLFK QYPYFNRKNI HIPNGDADDM NAEASKYNDV LEQQGQRDIQ ILGIGENGHI GFNEPGTPFD SVTHIVDLTE STIKANSRYF KNEDDVPKQA ISMGLANILQ AKRIILLAFG EKKRAAITHL LNQEISVDVP ATLLHKHPNV EIYLDDEACP KNVAKIHVDE MD

Experimental information

• Beam: Instrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia / Shape: Point / Type of source: X-ray synchrotron / Wavelength: 0.10332 Å / Dist. spec. to detc.: 1.6 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Staphylococcus aureus glucosamine-6-phosphate deaminase
Measurement date: Apr 26, 2016 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 999 / Unit: 1/A /

	Min	Max
Q	0.0121	0.6866

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 372 /

	Min	Max
Q	0.0216383	0.293513
P(R) point	1	372
R	0	89.22

Result

Type of curve: single_conc /

	Experimental	Porod
MW	56.4 kDa	53 kDa
Volume	-	84.2 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	0.06816	0.0679	0.0002
Radius of gyration, Rg	2.75 nm	2.725 nm	0.031

	Min	Max
D	-	8.92
Guinier point	14	47