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.


1sxq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:34, 14 February 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==BGT in complex with a 13mer DNA containing a central C:G base pair and UDP==
==BGT in complex with a 13mer DNA containing a central C:G base pair and UDP==
-
<StructureSection load='1sxq' size='340' side='right' caption='[[1sxq]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+
<StructureSection load='1sxq' size='340' side='right'caption='[[1sxq]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[1sxq]] is a 6 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=1SXQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SXQ FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[1sxq]] is a 6 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=1SXQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SXQ FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
+
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1m5r|1m5r]], [[1ixy|1ixy]], [[1sxp|1sxp]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BGT, BETA-GT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=1sxq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sxq OCA], [https://pdbe.org/1sxq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sxq RCSB], [https://www.ebi.ac.uk/pdbsum/1sxq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sxq ProSAT]</span></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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sxq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sxq OCA], [http://pdbe.org/1sxq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sxq RCSB], [http://www.ebi.ac.uk/pdbsum/1sxq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sxq 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 ==
+
-
Beta-glucosyltransferase (BGT) is a DNA-modifying enzyme and a glycosyltransferase. This inverting enzyme transfers glucose from UDP-glucose to the 5-hydroxymethyl cytosine bases of T4 phage DNA. From previous structural analyses we showed that Asp-100 and Asn-70 were, respectively, the catalytic base and the key residue for specific DNA recognition (Lariviere, L., Gueguen-Chaignon, V., and Morera, S. (2003) J. Mol. Biol. 330, 1077-1086). Here, we supply biochemical evidence supporting their essential roles in catalysis. We have also shown previously that BGT uses a base-flipping mechanism to access 5-hydroxymethyl cytosine (Lariviere, L., and Morera, S. (2002) J. Mol. Biol. 324, 483-490). Whether it is an active or a passive process remains unclear, as is the case for all DNA cleaving and modifying enzymes. Here, we report two crystal structures: (i) BGT in complex with a 13-mer DNA containing an A:G mismatch and (ii) BGT in a ternary complex with UDP and an oligonucleotide containing a single central G:C base pair. The binary structure reveals a specific complex with the flipped-out, mismatched adenine exposed to the active site. Unexpectedly, the other structure shows the non-productive binding of an intermediate flipped-out base. Our structural analysis provides clear evidence for a passive process.
+
-
 
+
-
Structural evidence of a passive base-flipping mechanism for beta-glucosyltransferase.,Lariviere L, Morera S J Biol Chem. 2004 Aug 13;279(33):34715-20. Epub 2004 Jun 3. PMID:15178685<ref>PMID:15178685</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 1sxq" 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: Lariviere, L]]
+
[[Category: Lariviere L]]
-
[[Category: Morera, S]]
+
[[Category: Morera S]]
-
[[Category: Flipped-out base]]
+
-
[[Category: Transferase-dna complex]]
+

Current revision

BGT in complex with a 13mer DNA containing a central C:G base pair and UDP

PDB ID 1sxq

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/1sxq"
Personal tools