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- SASDEA6: Staphylococcus aureus N-acetylglucosamine-6-phosphate deacetylase... -

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Basic information

Entry
Database: SASBDB / ID: SASDEA6
SampleStaphylococcus aureus N-acetylglucosamine-6-phosphate deacetylase dimer
  • N-acetylglucosamine-6-phosphate deacetylase (protein), NagA, Staphylococcus aureus (strain USA300)
Function / homology
Function and homology information


N-acetylglucosamine-6-phosphate deacetylase / N-acetylgalactosamine-6-phosphate deacetylase activity / N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine metabolic process / carbohydrate metabolic process / metal ion binding
Similarity search - Function
N-acetylglucosamine-6-phosphate deacetylase / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
N-acetylglucosamine-6-phosphate deacetylase
Similarity search - Component
Biological speciesStaphylococcus aureus (strain USA300) (bacteria)
CitationJournal: 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 ...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)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #2491
Type: atomic / Software: (2.0.6)
Comment: Structure of NagA isozyme from B subtilis fit to data. Generated using symmetry mates.
Chi-square value: 0.207
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Staphylococcus aureus N-acetylglucosamine-6-phosphate deacetylase dimer
Specimen concentration: 6 mg/ml
BufferName: 20 mM Tris-HCl 150 mM NaCl / pH: 8
Entity #1330Name: NagA / Type: protein / Description: N-acetylglucosamine-6-phosphate deacetylase / Formula weight: 43.115 / Num. of mol.: 2 / Source: Staphylococcus aureus (strain USA300) / References: UniProt: A0A0H2XGG9
Sequence: MSELIIYNGK VYTEDGKIDN GYIHVKDGQI VAIGEVDDKA AIDNDTTNKI QVIDAKGHHV LPGFIDIHIH GGYGQDAMDG SYDGLKYLSE NLLSEGTTSY LATTMTQSTD KIDNALTNIA KYEAEQDVHN AAEIVGIHLE GPFISENKVG AQHPQYVVRP FIDKIKHFQE ...Sequence:
MSELIIYNGK VYTEDGKIDN GYIHVKDGQI VAIGEVDDKA AIDNDTTNKI QVIDAKGHHV LPGFIDIHIH GGYGQDAMDG SYDGLKYLSE NLLSEGTTSY LATTMTQSTD KIDNALTNIA KYEAEQDVHN AAEIVGIHLE GPFISENKVG AQHPQYVVRP FIDKIKHFQE TANGLIKIMT FAPEVEGAKE ALETYKDDII FSIGHTVATY EEAVEAVERG AKHVTHLYNA ATPFQHREPG VFGAAWLNDA LHTEMIVDGT HSHPASVAIA YRMKGNERFY LITDAMRAKG MPEGEYDLGG QKVTVQSQQA RLANGALAGS ILKMNHGLRN LISFTGDTLD HLWRVTSLNQ AIALGIDDRK GSIKVNKDAD LVILDDDMNV KSTIKQGKVH TFS

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Experimental information

BeamInstrument 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
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Staphylococcus aureus N-acetylglucosamine-6-phosphate deacetylase dimer
Measurement date: Apr 26, 2016 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 999 / Unit: 1/A /
MinMax
Q0.0121 0.6866
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 322 /
MinMax
Q0.0179709 0.253262
P(R) point1 322
R0 101
Result
Type of curve: single_conc /
ExperimentalPorod
MW82.1 kDa67 kDa
Volume-107 nm3

P(R)GuinierGuinier error
Forward scattering, I00.05517 0.054922 0.0002
Radius of gyration, Rg3.19 nm3.158 nm0.008

MinMax
D-10.1
Guinier point9 40

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