This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1nvk

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 3: Line 3:
<StructureSection load='1nvk' size='340' side='right'caption='[[1nvk]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='1nvk' size='340' side='right'caption='[[1nvk]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[1nvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1NVK FirstGlance]. <br>
+
<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>
</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>
</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>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jg7|1jg7]], [[1jix|1jix]], [[1jiu|1jiu]]</div></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=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>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BGT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
+
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
+
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nvk OCA], [http://pdbe.org/1nvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nvk RCSB], [http://www.ebi.ac.uk/pdbsum/1nvk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nvk ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://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.
+
[[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.
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
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.
+
-
 
+
-
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:12860129<ref>PMID:12860129</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 1nvk" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bpt4]]
+
[[Category: Escherichia virus T4]]
-
[[Category: DNA beta-glucosyltransferase]]
+
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Gueguen-Chaignon, V]]
+
[[Category: Gueguen-Chaignon V]]
-
[[Category: Kurzeck, J]]
+
[[Category: Kurzeck J]]
-
[[Category: Lariviere, L]]
+
[[Category: Lariviere L]]
-
[[Category: Morera, S]]
+
[[Category: Morera S]]
-
[[Category: Rueger, W]]
+
[[Category: Rueger W]]
-
[[Category: Glycosyltransferase]]
+
-
[[Category: Gt-b]]
+
-
[[Category: Mn]]
+
-
[[Category: Transferase]]
+

Revision as of 17:01, 7 September 2022

T4 phage BGT in complex with UDP and a Mn2+ ion at 1.8 A resolution

PDB ID 1nvk

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nvk"
Personal tools