2z4t: Difference between revisions

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-{{Seed}}
-[[Image:2z4t.png|left|200px]]
-<!--
+==Crystal Structure of Vibrionaceae Photobacterium sp. JT-ISH-224 2,6-sialyltransferase in a Ternary Complex with Donor Product CMP and Accepter Substrate Lactose==
-The line below this paragraph, containing "STRUCTURE_2z4t", creates the "Structure Box" on the page.
+<StructureSection load='2z4t' size='340' side='right'caption='[[2z4t]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2z4t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Photobacterium_sp._JT-ISH-224 Photobacterium sp. JT-ISH-224]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z4T FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PRD_900008:alpha-lactose'>PRD_900008</scene></td></tr>
-{{STRUCTURE_2z4t|  PDB=2z4t  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z4t OCA], [https://pdbe.org/2z4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z4t RCSB], [https://www.ebi.ac.uk/pdbsum/2z4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z4t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A8QYL1_9GAMM A8QYL1_9GAMM]
+== 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/z4/2z4t_consurf.spt"</scriptWhenChecked>
+    <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/main_output.php?pdb_ID=2z4t ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Sialyltransferases are a family of glycosyltransferases that catalyze the transfer of N-acetylneuraminic acid residues from cytidine monophosphate N-acetylneuraminic acid (CMP-NeuAc) as a donor substrate to the carbohydrate groups of glycoproteins and glycolipids as acceptor substrates. We determined the crystal structure of Delta16psp26ST, the N-terminal truncated form of alpha2,6-sialyltransferase from Vibrionaceae Photobacterium sp. JT-ISH-224, complexed with a donor product CMP and an acceptor substrate lactose. Delta16psp26ST has three structural domains. Domain 1 belongs to the immunoglobulin-like beta-sandwich fold, and domains 2 and 3 form the glycosyltransferase-B structure. The CMP and lactose were bound in the deep cleft between domains 2 and 3. In the structure, only Asp232 was within hydrogen-binding distance of the acceptor O6 carbon of the galactose residue in lactose, and His405 was within hydrogen-binding distance of the phosphate oxygen of CMP. Mutation of these residues greatly decreased the activity of the enzyme. These structural and mutational results indicated that Asp232 might act as a catalytic base for deprotonation of the acceptor substrate, and His405 might act as a catalytic acid for protonation of the donor substrate. These findings are consistent with an in-line-displacement reaction mechanism in which Delta16psp26ST catalyzes the inverting transfer reaction. Unlike the case with multifunctional sialyltransferase (Delta24PmST1) complexed with CMP and lactose, the crystal structure of which was recently reported, the alpha2,6 reaction specificity of Delta16psp26ST is likely to be determined by His123.
-===Crystal Structure of Vibrionaceae Photobacterium sp. JT-ISH-224 2,6-sialyltransferase in a Ternary Complex with Donor Product CMP and Accepter Substrate Lactose===
+Crystal structure of Vibrionaceae Photobacterium sp. JT-ISH-224 alpha2,6-sialyltransferase in a ternary complex with donor product CMP and acceptor substrate lactose: catalytic mechanism and substrate recognition.,Kakuta Y, Okino N, Kajiwara H, Ichikawa M, Takakura Y, Ito M, Yamamoto T Glycobiology. 2008 Jan;18(1):66-73. Epub 2007 Oct 25. PMID:17962295<ref>PMID:17962295</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2z4t" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17962295}}, adds the Publication Abstract to the page
+*[[Sialyltransferase 3D structures|Sialyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17962295 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17962295}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Z4T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Photobacterium_sp. Photobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4T OCA].
+[[Category: Photobacterium sp. JT-ISH-224]]
+[[Category: Ichikawa M]]
-==Reference==
+[[Category: Ito M]]
-Crystal structure of Vibrionaceae Photobacterium sp. JT-ISH-224 alpha2,6-sialyltransferase in a ternary complex with donor product CMP and acceptor substrate lactose: catalytic mechanism and substrate recognition., Kakuta Y, Okino N, Kajiwara H, Ichikawa M, Takakura Y, Ito M, Yamamoto T, Glycobiology. 2008 Jan;18(1):66-73. Epub 2007 Oct 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17962295 17962295]
+[[Category: Kajiwara H]]
-[[Category: Photobacterium sp.]]
+[[Category: Kakuta Y]]
-[[Category: Single protein]]
+[[Category: Okino N]]
-[[Category: Ichikawa, M.]]
+[[Category: Takakura Y]]
-[[Category: Ito, M.]]
+[[Category: Yamamoto T]]
-[[Category: Kajiwara, H.]]
-[[Category: Kakuta, Y.]]
-[[Category: Okino, N.]]
-[[Category: Takakura, Y.]]
-[[Category: Yamamoto, T.]]
-[[Category: Glycosyltransferase]]
-[[Category: Gt-b fold]]
-[[Category: Immunoglobulin-like beta-sandwich fold]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 04:36:01 2008''