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1sxp

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Revision as of 13:58, 1 February 2024

BGT in complex with a 13mer DNA containing a central A:G mismatch

Structural highlights

1sxp is a 4 chain structure with sequence from Escherichia virus T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lariviere L, Morera S. Structural evidence of a passive base-flipping mechanism for beta-glucosyltransferase. J Biol Chem. 2004 Aug 13;279(33):34715-20. Epub 2004 Jun 3. PMID:15178685 doi:http://dx.doi.org/10.1074/jbc.M404394200

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1sxp"

Categories: Escherichia virus T4 | Large Structures | Lariviere L | Morera S

@@ Line 3: / Line 3: @@
 <StructureSection load='1sxp' size='340' side='right'caption='[[1sxp]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1sxp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SXP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SXP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1sxp]] is a 4 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=1SXP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SXP 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=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1m5r|1m5r]], [[1ixy|1ixy]], [[1sxq|1sxq]]</div></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=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BGT, BETA-GT ([https://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'>[https://en.wikipedia.org/wiki/DNA_beta-glucosyltransferase DNA beta-glucosyltransferase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=1sxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sxp OCA], [https://pdbe.org/1sxp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sxp RCSB], [https://www.ebi.ac.uk/pdbsum/1sxp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sxp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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.
+[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 ==
@@ Line 25: / Line 23: @@
 __TOC__
 </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]]

1sxp

From Proteopedia

Revision as of 13:58, 1 February 2024

BGT in complex with a 13mer DNA containing a central A:G mismatch

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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