SASDB33: Glutamate decarboxylase alpha (GadA) from E. coli (GadA)

Basic information

• Entry: Database: SASBDB / ID: SASDB33

Sample

Glutamate decarboxylase alpha (GadA) from E. coli

• Glutamate decarboxylase alpha (GadA) from E. coli (protein), GadA, Escherichia coli

Function / homology

Function:

glutamate decarboxylase / glutamate decarboxylase activity / glutamate catabolic process / intracellular pH elevation / pyridoxal phosphate binding / membrane / cytosol

Domain/homology:

Glutamate decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase

Component:

Glutamate decarboxylase alpha

• Biological species: Escherichia coli (E. coli)
• Citation: Journal: PLoS One / Year: 2016; Title: X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.; Authors: Liubov A Dadinova / Eleonora V Shtykova / Petr V Konarev / Elena V Rodina / Natalia E Snalina / Natalia N Vorobyeva / Svetlana A Kurilova / Tatyana I Nazarova / Cy M Jeffries / Dmitri I Svergun / ; Abstract: The structural analyses of four metabolic enzymes that maintain and regulate the stationary growth phase of Escherichia coli have been performed primarily drawing on the results obtained from solution small angle X-ray scattering (SAXS) and other structural techniques. The proteins are (i) class I fructose-1,6-bisphosphate aldolase (FbaB); (ii) inorganic pyrophosphatase (PPase); (iii) 5-keto-4-deoxyuronate isomerase (KduI); and (iv) glutamate decarboxylase (GadA). The enzyme FbaB, that until now had an unknown structure, is predicted to fold into a TIM-barrel motif that form globular protomers which SAXS experiments show associate into decameric assemblies. In agreement with previously reported crystal structures, PPase forms hexamers in solution that are similar to the previously reported X-ray crystal structure. Both KduI and GadA that are responsible for carbohydrate (pectin) metabolism and acid stress responses, respectively, form polydisperse mixtures consisting of different oligomeric states. Overall the SAXS experiments yield additional insights into shape and organization of these metabolic enzymes and further demonstrate the utility of hybrid methods, i.e., solution SAXS combined with X-ray crystallography, bioinformatics and predictive 3D-structural modeling, as tools to enrich structural studies. The results highlight the structural complexity that the protein components of metabolic networks may adopt which cannot be fully captured using individual structural biology techniques.

Contact author

• Liubov Dadinova (MSU, Lomonosov Moscow State University, Moscow, Russia)

Models

• Model #527: ; Type: mix / Radius of dummy atoms: 1.90 A / Symmetry: P32 / Chi-square value: 1.37 / P-value: 0.000032; Search similar-shape structures of this assembly by Omokage search (details)
• Model #528: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.37 / P-value: 0.000032; Search similar-shape structures of this assembly by Omokage search (details)
• Model #529: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.37 / P-value: 0.000032; Search similar-shape structures of this assembly by Omokage search (details)
• Model #530: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.37 / P-value: 0.000032; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Glutamate decarboxylase alpha (GadA) from E. coli / Specimen concentration: 1.40-10.80
• Buffer: Name: 50 mM Tris 10 mM NaCl / Concentration: 50.00 mM / pH: 7.5 / Composition: 10 mM NaCl

Entity #283

Name: GadA / Type: protein
Description: Glutamate decarboxylase alpha (GadA) from E. coli
Formula weight: 52.685 / Num. of mol.: 1 / Source: Escherichia coli / References: UniProt: P69908
Sequence:

MDQKLLTDFR SELLDSRFGA KAISTIAESK RFPLHEMRDD VAFQIINDEL YLDGNARQNL ATFCQTWDDE NVHKLMDLSI NKNWIDKEEY PQSAAIDLRC VNMVADLWHA PAPKNGQAVG TNTIGSSEAC MLGGMAMKWR WRKRMEAAGK PTDKPNLVCG PVQICWHKFA RYWDVELREI PMRPGQLFMD PKRMIEACDE NTIGVVPTFG VTYTGNYEFP QPLHDALDKF QADTGIDIDM HIDAASGGFL APFVAPDIVW DFRLPRVKSI SASGHKFGLA PLGCGWVIWR DEEALPQELV FNVDYLGGQI GTFAINFSRP AGQVIAQYYE FLRLGREGYT KVQNASYQVA AYLADEIAKL GPYEFICTGR PDEGIPAVCF KLKDGEDPGY TLYDLSERLR LRGWQVPAFT LGGEATDIVV MRIMCRRGFE MDFAELLLED YKASLKYLSD HPKLQGIAQQ NSFKHT

Experimental information

• Beam: Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Glutamate decarboxylase alpha (GadA) from E. coli / Measurement date: Jun 20, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.0794	4.5675

Result

Type of curve: single_conc
Comments: Under the experimental conditions described above, GadA exists as a mixture in solution of likely hexamers (volume fraction approximately 60%) and disassociated dimers (40%). The models displayed for this entry and associated fit are derived from SASREFMX modelling in P32 symmetry. The final fit to the SAXS data of the mixture was determined using OLIGOMER. The specific volume fraction estimates of the hexamer and three dimers are included in the full entry zip archive.

	Experimental	Standard	Porod
MW	249 kDa	249 kDa	241 kDa
Volume	-	-	410 nm3

	Guinier	Guinier error
Forward scattering, I0	14105	23.5
Radius of gyration, Rg	4.8 nm	0.02

	Min	Max
Guinier point	3	71