4PPH

Crystal structure of conglutin gamma, a unique basic 7S globulin from lupine seeds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structure of gamma-conglutin: insight into the quaternary structure of 7S basic globulins from legumes.

Czubinski, J.Barciszewski, J.Gilski, M.Szpotkowski, K.Debski, J.Lampart-Szczapa, E.Jaskolski, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 224-238

  • DOI: 10.1107/S1399004714025073
  • Primary Citation of Related Structures:  
    4PPH

  • PubMed Abstract: 
  • γ-Conglutin from lupin seeds is an unusual 7S basic globulin protein. It is capable of reducing glycaemia in mammals, but the structural basis of this activity is not known. γ-Conglutin shares a high level of structural homology with glycoside hydrolase inhibitor proteins, although it lacks any kind of inhibitory activity against plant cell-wall degradation enzymes ...

    γ-Conglutin from lupin seeds is an unusual 7S basic globulin protein. It is capable of reducing glycaemia in mammals, but the structural basis of this activity is not known. γ-Conglutin shares a high level of structural homology with glycoside hydrolase inhibitor proteins, although it lacks any kind of inhibitory activity against plant cell-wall degradation enzymes. In addition, γ-conglutin displays a less pronounced structural similarity to pepsin-like aspartic proteases, but it is proteolytically dysfunctional. Only one structural study of a legume 7S basic globulin, that isolated from soybean, has been reported to date. The quaternary assembly of soybean 7S basic globulin (Bg7S) is arranged as a cruciform-shaped tetramer comprised of two superposed dimers. Here, the crystal structure of γ-conglutin isolated from Lupinus angustifolius seeds (LangC) is presented. The polypeptide chain of LangC is post-translationally cleaved into α and β subunits but retains its covalent integrity owing to a disulfide bridge. The protomers of LangC undergo an intricate quaternary assembly, resulting in a ring-like hexamer with noncrystallographic D3 symmetry. The twofold-related dimers are similar to those in Bg7S but their assembly is different as a consequence of mutations in a β-strand that is involved in intermolecular β-sheet formation in γ-conglutin. Structural elucidation of γ-conglutin will help to explain its physiological role, especially in the evolutionary context, and will guide further research into the hypoglycaemic activity of this protein in humans, with potential consequences for novel antidiabetic therapies.


    Related Citations: 
    • Characterisation of different digestion susceptibility of lupin seed globulins.
      Czubinski, J., Dwiecki, K., Siger, A., Neunert, G., Lampart-Szczapa, E.
      (2014) Food Chem 143: 418
    • Release of flavonoids from lupin globulin proteins during digestion in a model system.
      Czubinski, J., Dwiecki, K., Siger, A., Kachlicki, P., Neunert, G., Lampart-Szczapa, E., Nogala-Kalucka, M.
      (2012) J Agric Food Chem 60: 1830
    • Crystal structure of basic 7S globulin, a xyloglucan-specific endo-beta-1,4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-beta-glucanase.
      Yoshizawa, T., Shimizu, T., Yamabe, M., Taichi, M., Nishiuchi, Y., Shichijo, N., Unzai, S., Hirano, H., Sato, M., Hashimoto, H.
      (2011) FEBS J 278: 1944
    • Internalisation and multiple phosphorylation of gamma-Conglutin, the lupin seed glycaemia-lowering protein, in HepG2 cells.
      Capraro, J., Magni, C., Faoro, F., Maffi, D., Scarafoni, A., Tedeschi, G., Maffioli, E., Parolari, A., Manzoni, C., Lovati, M.R., Duranti, M.
      (2013) Biochem Biophys Res Commun 437: 648
    • Lupin seed gamma-conglutin lowers blood glucose in hyperglycaemic rats and increases glucose consumption of HepG2 cells.
      Lovati, M.R., Manzoni, C., Castiglioni, S., Parolari, A., Magni, C., Duranti, M.
      (2012) Br J Nutr 107: 67

    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Conglutin gamma
A, B, C, D, E, F
A, B, C, D, E, F
417Lupinus angustifoliusMutation(s): 0 
Gene Names: LOC109345795TanjilG_29300
UniProt
Find proteins for Q42369 (Lupinus angustifolius)
Explore Q42369 
Go to UniProtKB:  Q42369
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ42369
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranoseG 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G11971MR
GlyCosmos:  G11971MR
GlyGen:  G11971MR
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D],
O [auth B],
U [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth E],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
N [auth A],
NA [auth F],
OA [auth F],
P [auth B],
PA [auth F],
Q [auth B],
QA [auth F],
R [auth B],
S [auth B],
T [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.99α = 90
b = 121.99β = 90
c = 188.49γ = 120
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Advisory, Database references, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary