Sandbox1503: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Loïc Plessis

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-==3vuf Protein(title here)==
+=3vuf=
 <StructureSection load='3vuf' size='340' side='right' caption='[[3vuf]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-This is a default text for your page '''Sandbox1503'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
+vuf is a 1 chain structure protein which is synthesized by the Japanese rice (Oryza sativa japonica). it’s an enzyme, more accurately a transferase. It’s a NDP-glucose--starch glucosyltransferase, which is involved in the synthesis of amylose in the rice. This enzyme is located chloroplast and in amyloplast.
-You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
+The 3vuf protein is 609 amino acids long and weighs 66 476 Da.
 == Function ==
-[[http://www.uniprot.org/uniprot/SSG1_ORYSJ SSG1_ORYSJ]] Required for the synthesis of amylose in endosperm.[HAMAP-Rule:MF_00484]
+The protein have a role of transferase, more accurately it is a NDP-glucose--starch glucosyltransferase, which catalyse the reaction below :
-<div style="background-color:#fffaf0;">
+[[Image:Catalytic activity 3vuf'.jpg|900px|]]
-== Publication Abstract from PubMed ==
-The catalytic domain of rice (Oryza sativa japonica) granule bound starch synthase I (OsGBSSI-CD) was overexpressed and the three-dimensional structures of the ligand-free and ADP-bound forms were determined. The structures were similar to those reported for bacterial and archaeal glycogen synthases, which belong to glycosyltransferase family 5. They had Rossmann fold N- and C-domains connected by canonical two-hinge peptides, and an interdomain disulfide bond that appears to be conserved in the Poaceae plant family. The presence of three covalent linkages might explain why both OsGBSSI-CD structures adopted only the closed domain arrangement.
-Interdomain Disulfide Bridge in the Rice Granule Bound Starch Synthase I Catalytic Domain as Elucidated by X-Ray Structure Analysis.,Momma M, Fujimoto Z Biosci Biotechnol Biochem. 2012 Aug 7. PMID:22878205<ref>PMID:22878205</ref>
+This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3vuf" style="background-color:#fffaf0;"></div>
-== Disease ==
+[[http://www.uniprot.org/uniprot/SSG1_ORYSJ SSG1_ORYSJ]] Required for the synthesis of amylose in endosperm.[HAMAP-Rule:MF_00484]
-The protein 3vuf has '''allergenic properties''', for example in mammals it can bind to Immunoglobulin E (IgE) causing an allergic response.
+<div style="background-color:#fffaf0;">
-== Relevance ==
+== Structural highlights ==
+This protein is an enzyme, which is formed from one monomer and can bind to ADP. It binds to the ADP-glucose with amino acids 97,100, 408, 413,462 and 492. This allow the formation of an hydrophobic pocket in which ADP-glucose can binds to and in which he is protected from water and hydrolyse. we can also see that 3vuf can binds sulfate. This hydrophobic cage is allowed by the beta sheets and alpha helices that the protein have.
-== Amino Acid Sequence ==
-== Structural highlights ==
 <table><tr><td colspan='2'>[[3vuf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VUF FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
@@ Line 33: / Line 25: @@
 </table>
 This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
+== Structure ==
+'''Primary structure (amino acid sequence):
+'''
+MSALTTSQLA TSATGFGIAD RSAPSSLLRH GFQGLKPRSP AGGDATSLSV
+TTSARATPKQ QRSVQRGSRR FPSVVVYATG AGMNVVFVGA EMAPWSKTGG
+LGDVLGGLPP AMAANGHRVM VISPRYDQYK DAWDTSVVAE IKVADRYERV
+RFFHCYKRGV DRVFIDHPSF LEKVWGKTGE KIYGPDTGVD YKDNQMRFSL
+LCQAALEAPR ILNLNNNPYF KGTYGEDVVF VCNDWHTGPL ASYLKNNYQP
+NGIYRNAKVA FCIHNISYQG RFAFEDYPEL NLSERFRSSF DFIDGYDTPV
+EGRKINWMKA GILEADRVLT VSPYYAEELI SGIARGCELD NIMRLTGITG
+IVNGMDVSEW DPSKDKYITA KYDATTAIEA KALNKEALQA EAGLPVDRKI
+PLIAFIGRLE EQKGPDVMAA AIPELMQEDV QIVLLGTGKK KFEKLLKSME
+EKYPGKVRAV VKFNAPLAHL IMAGADVLAV PSRFEPCGLI QLQGMRYGTP
+CACASTGGLV DTVIEGKTGF HMGRLSVDCK VVEPSDVKKV AATLKRAIKV
+VGTPAYEEMV RNCMNQDLSW KGPAKNWENV LLGLGVAGSA PGIEGDEIAP
+LAKENVAAP
+'''Secondary structure:'''
+[[Image:oui.jpg|900px|]]
+==Relevance==
+Amylose synthesis allows to the plant having some provisions, for a future seed or for some organ for passing bad seasons. In the rice, it is for a future seed, which is the rice itself. In this forme, amylose is chemically stable. This means that it can’t react except by depolymerisation or polymerisation, but not for producing bioenergy, like ATP or any others. Another property of this form of glucose, is that it doesn’t modify the chemical potential of the cell, which is very good and doesn’t unsettle the equilibrium of the cell.
+== Disease ==
+The protein 3vuf has '''allergenic properties''', for example in mammals it can bind to Immunoglobulin E (IgE) causing an allergic response.
 </StructureSection>
 == References ==
-<references/>
-__TOC__
+(1) Momma M, Fujimoto Z. Interdomain Disulfide Bridge in the Rice Granule Bound Starch Synthase I Catalytic Domain as Elucidated by X-Ray Structure Analysis. Biosci Biotechnol Biochem. 2012 Aug 7. PMID:22878205
-</StructureSection>
 [[Category: Japanese rice]]
 [[Category: NDP-glucose--starch glucosyltransferase]]