2d5f

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Recombinant Soybean Proglycinin A3B4 subunit, its Comparison with Mature Glycinin A3B4 subunit, Responsible for Hexamer Assembly

Structural highlights

2d5f 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 1.9Å
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

The crystal structures of two pro-11S globulins namely: rapeseed procruciferin and pea prolegumin are presented here. We have extensively compared them with the other known structures of plant seed 11S and 7S globulins. In general, the disordered regions in the crystal structures among the 11S globulins correspond to their five variable regions. Variable region III of procruciferin is relatively short and is in a loop conformation. This region is highly disordered in other pro-11S globulin crystals. Local helical and strand variations also occur across the group despite general structure conservation. We showed how these variations may alter specific physicochemical, functional and physiological properties. Aliphatic hydrophobic residues on the molecular surface correlate well with Tm values of the globulins. We also considered other structural features that were reported to influence thermal stability but no definite conclusion was drawn since each factor has additive or subtractive effect. Comparison between proA3B4 and mature A3B4 revealed an increase in r.m.s.d. values near variable regions II and IV. Both regions are on the IE face. Secondary structure based alignment of 11S and 7S globulins revealed 16 identical residues. Based on proA3B4 sequence, Pro60, Gly128, Phe163, Phe208, Leu213, Leu227, Ile237, Pro382, Val404, Pro425 and Val 466 are involved in trimer formation and stabilization. Gly28, Gly74, Asp135, Gly349 and Gly397 are involved in correct globular folding.

Conservation and divergence on plant seed 11S globulins based on crystal structures.,Tandang-Silvas MR, Fukuda T, Fukuda C, Prak K, Cabanos C, Kimura A, Itoh T, Mikami B, Utsumi S, Maruyama N Biochim Biophys Acta. 2010 Jul;1804(7):1432-42. Epub 2010 Mar 6. PMID:20215054^[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
↑ Tandang-Silvas MR, Fukuda T, Fukuda C, Prak K, Cabanos C, Kimura A, Itoh T, Mikami B, Utsumi S, Maruyama N. Conservation and divergence on plant seed 11S globulins based on crystal structures. Biochim Biophys Acta. 2010 Jul;1804(7):1432-42. Epub 2010 Mar 6. PMID:20215054 doi:10.1016/j.bbapap.2010.02.016

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/2d5f"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Recombinant Soybean Proglycinin A3B4 subunit, its Comparison with Mature Glycinin A3B4 subunit, Responsible for Hexamer Assembly==
-<StructureSection load='2d5f' size='340' side='right' caption='[[2d5f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2d5f' size='340' side='right'caption='[[2d5f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2d5f]] 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=2D5F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D5F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2d5f]] 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=2D5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D5F 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]] 1.9&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></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=CSD:3-SULFINOALANINE'>CSD</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d5f OCA], [http://pdbe.org/2d5f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d5f RCSB], [http://www.ebi.ac.uk/pdbsum/2d5f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d5f ProSAT]</span></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=2d5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d5f OCA], [https://pdbe.org/2d5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d5f RCSB], [https://www.ebi.ac.uk/pdbsum/2d5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d5f 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]]
@@ Line 13: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d5/2d5f_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>
@@ Line 32: / Line 34: @@
 </StructureSection>
 [[Category: Glycine max]]
-[[Category: Adachi, M]]
+[[Category: Large Structures]]
-[[Category: Itoh, T]]
+[[Category: Adachi M]]
-[[Category: Masuda, T]]
+[[Category: Itoh T]]
-[[Category: Mikami, B]]
+[[Category: Masuda T]]
-[[Category: Utsumi, S]]
+[[Category: Mikami B]]
-[[Category: Globulin]]
+[[Category: Utsumi S]]
-[[Category: Glycinin]]
-[[Category: Plant protein]]
-[[Category: Seed storage protein]]
-[[Category: Soybean]]

2d5f

From Proteopedia

Current revision

Crystal Structure of Recombinant Soybean Proglycinin A3B4 subunit, its Comparison with Mature Glycinin A3B4 subunit, Responsible for Hexamer Assembly

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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