1rrv

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:07, 23 August 2023) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1rrv.png|left|200px]]
 
-
<!--
+
==X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.==
-
The line below this paragraph, containing "STRUCTURE_1rrv", creates the "Structure Box" on the page.
+
<StructureSection load='1rrv' size='340' side='right'caption='[[1rrv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1rrv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RRV FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</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&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3FG:(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC+ACID'>3FG</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GHP:(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC+ACID'>GHP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MLU:N-METHYL-D-LEUCINE'>MLU</scene>, <scene name='pdbligand=OMY:(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE'>OMY</scene>, <scene name='pdbligand=OMZ:(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE'>OMZ</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
-
{{STRUCTURE_1rrv| PDB=1rrv | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrv OCA], [https://pdbe.org/1rrv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rrv RCSB], [https://www.ebi.ac.uk/pdbsum/1rrv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rrv ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/GTFD_AMYOR GTFD_AMYOR] Catalyzes the attachment of L-vancosamine to a monoglucosylated heptapeptide intermediate during the final stage of glycopeptide antibiotic vancomycin biosynthesis.<ref>PMID:11294642</ref> <ref>PMID:15122882</ref>
 +
== 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/rr/1rrv_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1rrv ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The TDP-vancosaminyltransferase GtfD catalyzes the attachment of L-vancosamine to a monoglucosylated heptapeptide intermediate during the final stage of vancomycin biosynthesis. Glycosyltransferases from this and similar antibiotic pathways are potential tools for the design of new compounds that are effective against vancomycin resistant bacterial strains. We have determined the X-ray crystal structure of GtfD as a complex with TDP and the natural glycopeptide substrate at 2.0 A resolution. GtfD, a member of the bidomain GT-B glycosyltransferase superfamily, binds TDP in the interdomain cleft, while the aglycone acceptor binds in a deep crevice in the N-terminal domain. However, the two domains are more interdependent in terms of substrate binding and overall structure than was evident in the structures of closely related glycosyltransferases GtfA and GtfB. Structural and kinetic analyses support the identification of Asp13 as a catalytic general base, with a possible secondary role for Thr10. Several residues have also been identified as being involved in donor sugar binding and recognition.
-
===X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.===
+
Crystal structure of vancosaminyltransferase GtfD from the vancomycin biosynthetic pathway: interactions with acceptor and nucleotide ligands.,Mulichak AM, Lu W, Losey HC, Walsh CT, Garavito RM Biochemistry. 2004 May 11;43(18):5170-80. PMID:15122882<ref>PMID:15122882</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1rrv" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_15122882}}, adds the Publication Abstract to the page
+
*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 15122882 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_15122882}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
[[1rrv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRV OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:015122882</ref><references group="xtra"/>
+
[[Category: Amycolatopsis orientalis]]
[[Category: Amycolatopsis orientalis]]
-
[[Category: Garavito, R M.]]
+
[[Category: Large Structures]]
-
[[Category: Losey, H C.]]
+
[[Category: Garavito RM]]
-
[[Category: Lu, W.]]
+
[[Category: Losey HC]]
-
[[Category: Mulichak, A M.]]
+
[[Category: Lu W]]
-
[[Category: Walsh, C T.]]
+
[[Category: Mulichak AM]]
-
[[Category: Antibiotic]]
+
[[Category: Walsh CT]]
-
[[Category: Glycopeptide]]
+
-
[[Category: Glycosyltransferase]]
+
-
[[Category: Gt-b]]
+
-
[[Category: Rossmann fold]]
+
-
[[Category: Transferase-antibiotic complex]]
+
-
[[Category: Vacosamycin]]
+

Current revision

X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.

PDB ID 1rrv

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/1rrv"
Personal tools