SASDBZ2: Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli

Basic information

• Entry: Database: SASBDB / ID: SASDBZ2

Sample

Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli

• Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli (protein), FbaB, Escherichia coli

• Function / homology: :
• 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 #421: ; Type: dummy / Software: DAMMIN / Radius of dummy atoms: 2.80 A / Symmetry: P52 / Chi-square value: 1.232 / P-value: 0.000210; Search similar-shape structures of this assembly by Omokage search (details)
• Model #422: ; Type: atomic / Software: CORAL / Radius of dummy atoms: 1.90 A / Symmetry: P52 / Chi-square value: 1.809; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli; Specimen concentration: 1.40-10.80
• Buffer: Name: Tris / Concentration: 50.00 mM / pH: 7.5 / Composition: 10 mM NaCl

Entity #280

Name: FbaB / Type: protein
Description: Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli
Formula weight: 38.056 / Num. of mol.: 10 / Source: Escherichia coli / References: UniProt: A0A0K4BP99
Sequence:

MTDIAQLLGK DADNLLQHCC MTIPSDQLYL PGHDYVDRVM IDNNRPPAVL RNMQTLYNTG RLAGTGYLSI LPVDQGVEHS AGASFAANPL YFDPKNIVEL AIEAGCNCVA STYGVLASVS RRYAHRIPFL VKLNHNETLS YPNTYDQTLY ASVEQAFNMG AVAVGATIYF GSEESRRQIE EISAAFERAH ELGMVTVLWA YLRNSAFKKD GVDYHVSADL TGQANHLAAT IGADIVKQKM AENNGGYKAI NYGYTDDRVY SKLTSENPID LVRYQLANCY MGRAGLINSG GAAGGETDLS DAVRTAVINK RAGGMGLILG RKAFKKSMAD GVKLINAVQD VYLDSKITIA

Experimental information

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

Scan

Title: E. coli fructose-bisphosphate aldolase (fbaB) / Measurement date: Jun 30, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.0847	3.2337

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 1100 /

	Min	Max
Q	0.0846518	2.97585
P(R) point	1	1100
R	0	12.73

Result

Type of curve: single_conc
Comments: The models displayed above are, from top to bottom: 1) An individual DAMMIN dummy atom model and; 2) CORAL rigid body model with the associated CRYSOL fit to the data. All of the individual DAMMIN models and associated fits can be found in the zip archive for this entry along with the CORAL modelling results.

	Experimental	Standard	Porod
MW	340 kDa	340 kDa	302 kDa
Volume	-	-	484 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	16670	18	16826	25
Radius of gyration, Rg	4.34 nm	0.04	4.43 nm	0.02

	Min	Max
D	-	12.73
Guinier point	2	81