+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDBZ2 |
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Sample | Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli
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Function / homology | : Function and homology information |
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 ...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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-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) |
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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 |
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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 ...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 | ||||||||||||||||||||||||||||||||||||
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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 /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 1100 /
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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 ...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.
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