1nvk: Difference between revisions

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OCA

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-[[Image:1nvk.jpg|left|200px]]<br /><applet load="1nvk" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1nvk, resolution 1.8&Aring;" />
-'''T4 phage BGT in complex with UDP and a Mn2+ ion at 1.8 A resolution'''<br />
-==Overview==
+==T4 phage BGT in complex with UDP and a Mn2+ ion at 1.8 A resolution==
-T4 phage beta-glucosyltransferase (BGT) is an inverting, glycosyltransferase (GT) that transfers glucose from uridine, diphospho-glucose (UDP-glucose) to an acceptor modified DNA. BGT belongs, to the GT-B structural superfamily, represented, so far, by five different, inverting or retaining GT families. Here, we report three high-resolution, X-ray structures of BGT and a point mutant solved in the presence of, UDP-glucose. The two co-crystal structures of the D100A mutant show that, unlike the wild-type enzyme, this mutation prevents glucose hydrolysis., This strongly indicates that Asp100 is the catalytic base. We obtained the, wild-type BGT-UDP-glucose complex by soaking substrate-free BGT crystals., Comparison with a previous structure of BGT solved in the presence of the, donor product UDP and an acceptor analogue provides the first model of an, inverting GT-B enzyme in which both the donor and acceptor substrates are, bound to the active site. The structural analyses support the in-line, displacement reaction mechanism previously proposed, locate residues, involved in donor substrate specificity and identify the catalytic base.
+<StructureSection load='1nvk' size='340' side='right'caption='[[1nvk]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1nvk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NVK FirstGlance]. <br>
-NVK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with MN, UDP and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA_beta-glucosyltransferase DNA beta-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.27 2.4.1.27] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NVK OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nvk OCA], [https://pdbe.org/1nvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nvk RCSB], [https://www.ebi.ac.uk/pdbsum/1nvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nvk ProSAT]</span></td></tr>
-Crystal structures of the T4 phage beta-glucosyltransferase and the D100A mutant in complex with UDP-glucose: glucose binding and identification of the catalytic base for a direct displacement mechanism., Lariviere L, Gueguen-Chaignon V, Morera S, J Mol Biol. 2003 Jul 25;330(5):1077-86. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12860129 12860129]
+</table>
-[[Category: Bacteriophage t4]]
+== Function ==
-[[Category: DNA beta-glucosyltransferase]]
+[https://www.uniprot.org/uniprot/GSTB_BPT4 GSTB_BPT4] Catalyzes the transfer of glucose (Glc) from uridine diphosphoglucose (UDP-Glc) to 5-hydroxymethylcytosine (5-HMC) in double-stranded DNA. Is involved in a DNA modification process to protect the phage genome against its own nucleases and the host restriction endonuclease system.
-[[Category: Single protein]]
+__TOC__
-[[Category: Gueguen-Chaignon, V.]]
+</StructureSection>
-[[Category: Kurzeck, J.]]
+[[Category: Escherichia virus T4]]
-[[Category: Lariviere, L.]]
+[[Category: Large Structures]]
-[[Category: Morera, S.]]
+[[Category: Gueguen-Chaignon V]]
-[[Category: Rueger, W.]]
+[[Category: Kurzeck J]]
-[[Category: GOL]]
+[[Category: Lariviere L]]
-[[Category: MN]]
+[[Category: Morera S]]
-[[Category: UDP]]
+[[Category: Rueger W]]
-[[Category: glycosyltransferase]]
-[[Category: gt-b]]
-[[Category: mn]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:35:31 2007''