2fyb: Difference between revisions

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-[[Image:2fyb.png|left|200px]]
-{{STRUCTURE_2fyb|  PDB=2fyb  |  SCENE=  }}
+==Crystal structure of the catalytic domain of the human beta1,4-galactosyltransferase mutant M339H in complex with Mn and UDP-galactose in open conformation==
+<StructureSection load='2fyb' size='340' side='right'caption='[[2fyb]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2fyb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FYB FirstGlance]. <br>
+</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=2fyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fyb OCA], [https://pdbe.org/2fyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fyb RCSB], [https://www.ebi.ac.uk/pdbsum/2fyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fyb ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/B4GT1_HUMAN B4GT1_HUMAN] Defects in B4GALT1 are the cause of congenital disorder of glycosylation type 2D (CDG2D) [MIM:[https://omim.org/entry/607091 607091]. CDGs are a family of severe inherited diseases caused by a defect in protein N-glycosylation. They are characterized by under-glycosylated serum proteins. These multisystem disorders present with a wide variety of clinical features, such as disorders of the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions.
+== Function ==
+[https://www.uniprot.org/uniprot/B4GT1_HUMAN B4GT1_HUMAN] The Golgi complex form catalyzes the production of lactose in the lactating mammary gland and could also be responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids.  The cell surface form functions as a recognition molecule during a variety of cell to cell and cell to matrix interactions, as those occurring during development and egg fertilization, by binding to specific oligosaccharide ligands on opposing cells or in the extracellular matrix.
+== 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/fy/2fyb_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=2fyb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+During the catalytic cycle of beta1,4-galactosyltransferase-1 (Gal-T1), upon the binding of Mn(2+) followed by UDP-Gal, two flexible loops, a long and a short loop, change their conformation from open to closed. We have determined the crystal structures of a human M340H-Gal-T1 mutant in the open conformation (apo-enzyme), its Mn(2+) and Mn(2+)-UDP-Gal-bound complexes, and of a pentenary complex of bovine Gal-T1-Mn(2+)-UDP-GalNAc-Glc-alpha-lactalbumin. These studies show that during the conformational changes in Gal-T1, the coordination of Mn(2+) undergoes significant changes. It loses a coordination bond with a water molecule bound in the open conformation of Gal-T1 while forming a new coordination bond with another water molecule in the closed conformation, creating an active ground-state structure that facilitates enzyme catalysis. In the crystal structure of the pentenary complex, the N-acetylglucosamine (GlcNAc) moiety is found cleaved from UDP-GalNAc and is placed 2.7A away from the O4 oxygen atom of the acceptor Glc molecule, yet to form the product. The anomeric C1 atom of the cleaved GalNAc moiety has only two covalent bonds with its non-hydrogen atoms (O5 and C2 atoms), similar to either an oxocarbenium ion or N-acetylgalactal form, which are crystallographically indistinguishable at the present resolution. The structure also shows that the newly formed, metal-coordinating water molecule forms a hydrogen bond with the beta-phosphate group of the cleaved UDP moiety. This hydrogen bond formation results in the rotation of the beta-phosphate group of UDP away from the cleaved GalNAc moiety, thereby preventing the re-formation of the UDP-sugar during catalysis. Therefore, this water molecule plays an important role during catalysis in ensuring that the catalytic reaction proceeds in a forward direction.
-===Crystal structure of the catalytic domain of the human beta1,4-galactosyltransferase mutant M339H in complex with Mn and UDP-galactose in open conformation===
+Structural snapshots of beta-1,4-galactosyltransferase-I along the kinetic pathway.,Ramakrishnan B, Ramasamy V, Qasba PK J Mol Biol. 2006 Apr 14;357(5):1619-33. Epub 2006 Feb 9. PMID:16497331<ref>PMID:16497331</ref>
-{{ABSTRACT_PUBMED_16497331}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2fyb" style="background-color:#fffaf0;"></div>
-[[2fyb]] is a 1 chain structure of [[Galactosyltransferase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FYB OCA].
 ==See Also==
-*[[Galactosyltransferase|Galactosyltransferase]]
+*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016497331</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: N-acetyllactosamine synthase]]
+[[Category: Large Structures]]
-[[Category: Qasba, P K.]]
+[[Category: Qasba PK]]
-[[Category: Ramakrishnan, B.]]
+[[Category: Ramakrishnan B]]
-[[Category: Ramasamy, V.]]
+[[Category: Ramasamy V]]
-[[Category: Complex with udp-galactose and mn]]
-[[Category: M339h mutant]]
-[[Category: Open conformation]]
-[[Category: Transferase]]