1od5

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of glycinin A3B4 subunit homohexamer

Structural highlights

1od5 is a 2 chain structure with sequence from Glycine max. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLYG5_SOYBN Glycinin is the major seed storage protein of soybean (PubMed:2485233). Glycinin basic peptides (GBPs), and, to a lower extent, glycinin exhibit antibacterial activity against Gram-negative and Gram-positive bacteria (e.g. L.monocytogenes, B.subtilis, E.coli and S.enteritidis) by forming pores and aggregating in transmembranes, leading to membrane permeability and, eventually, cell death (PubMed:22236762, PubMed:28590128, Ref.15).^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Most plant seeds contain 11S globulins as major storage proteins for their nutrition. Soybean glycinin belongs to the 11S globulin family and consists of five kinds of subunits. We determined the crystal structure of a homohexamer of the glycinin A3B4 subunit at 2.1-A resolution. The crystal structure shows that the hexamer has 32-point group symmetry formed by face-to-face stacking of two trimers. The interface buries the highly conserved interchain disulfide. Based on the structure, we propose that an ingenious face-to-face mechanism controls the hexamer formation of the 11S globulin by movement of a mobile disordered region to the side of the trimer after posttranslational processing. Electrostatic analysis of the faces suggests that the interchain disulfide-containing face has high positive potential at acidic pH, which induces dissociation of the hexamer into trimers that may be susceptible to proteinases after seed imbibition. This dissociation might result in the degradation and mobilization of 11S globulins as storage proteins in embryos during germination and seedling growth.

Crystal structure of soybean 11S globulin: glycinin A3B4 homohexamer.,Adachi M, Kanamori J, Masuda T, Yagasaki K, Kitamura K, Mikami B, Utsumi S Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7395-400. Epub 2003 May 27. PMID:12771376^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sitohy MZ, Mahgoub SA, Osman AO. In vitro and in situ antimicrobial action and mechanism of glycinin and its basic subunit. Int J Food Microbiol. 2012 Mar 1;154(1-2):19-29. PMID:22236762 doi:10.1016/j.ijfoodmicro.2011.12.004
↑ Nielsen NC, Dickinson CD, Cho TJ, Thanh VH, Scallon BJ, Fischer RL, Sims TL, Drews GN, Goldberg RB. Characterization of the glycinin gene family in soybean. Plant Cell. 1989 Mar;1(3):313-28. PMID:2485233 doi:10.1105/tpc.1.3.313
↑ Zhao GP, Li YQ, Sun GJ, Mo HZ. Antibacterial Actions of Glycinin Basic Peptide against Escherichia coli. J Agric Food Chem. 2017 Jun 28;65(25):5173-5180. PMID:28590128 doi:10.1021/acs.jafc.7b02295
↑ González-Montoya M, Hernández-Ledesma B, Silván JM, Mora-Escobedo R, Martínez-Villaluenga C. Peptides derived from in vitro gastrointestinal digestion of germinated soybean proteins inhibit human colon cancer cells proliferation and inflammation. Food Chem. 2018 Mar 1;242:75-82. PMID:29037738 doi:10.1016/j.foodchem.2017.09.035
↑ Adachi M, Kanamori J, Masuda T, Yagasaki K, Kitamura K, Mikami B, Utsumi S. Crystal structure of soybean 11S globulin: glycinin A3B4 homohexamer. Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7395-400. Epub 2003 May 27. PMID:12771376 doi:10.1073/pnas.0832158100

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1od5"

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF GLYCININ A3B4 SUBUNIT HOMOHEXAMER==
-<StructureSection load='1od5' size='340' side='right' caption='[[1od5]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+==Crystal structure of glycinin A3B4 subunit homohexamer==
+<StructureSection load='1od5' size='340' side='right'caption='[[1od5]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1od5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OD5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1od5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OD5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1od5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1od5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1od5 RCSB], [http://www.ebi.ac.uk/pdbsum/1od5 PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1od5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1od5 OCA], [https://pdbe.org/1od5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1od5 RCSB], [https://www.ebi.ac.uk/pdbsum/1od5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1od5 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLYG5_SOYBN GLYG5_SOYBN] Glycinin is the major seed storage protein of soybean (PubMed:2485233). Glycinin basic peptides (GBPs), and, to a lower extent, glycinin exhibit antibacterial activity against Gram-negative and Gram-positive bacteria (e.g. L.monocytogenes, B.subtilis, E.coli and S.enteritidis) by forming pores and aggregating in transmembranes, leading to membrane permeability and, eventually, cell death (PubMed:22236762, PubMed:28590128, Ref.15).<ref>PMID:22236762</ref> <ref>PMID:2485233</ref> <ref>PMID:28590128</ref> <ref>PMID:29037738</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/od/1od5_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/od/1od5_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1od5 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1od5" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 29: / Line 34: @@
 </StructureSection>
 [[Category: Glycine max]]
-[[Category: Adachi, M]]
+[[Category: Large Structures]]
-[[Category: Kanamori, J]]
+[[Category: Adachi M]]
-[[Category: Kitamura, K]]
+[[Category: Kanamori J]]
-[[Category: Masuda, T]]
+[[Category: Kitamura K]]
-[[Category: Mikami, B]]
+[[Category: Masuda T]]
-[[Category: Utsumi, S]]
+[[Category: Mikami B]]
-[[Category: Yagasaki, K]]
+[[Category: Utsumi S]]
-[[Category: Globulin]]
+[[Category: Yagasaki K]]
-[[Category: Glycinin]]
-[[Category: Seed storage protein]]
-[[Category: Soybean]]

1od5

From Proteopedia

Current revision

Crystal structure of glycinin A3B4 subunit homohexamer

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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