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4ax8

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Medium resolution structure of the bifunctional kinase- methyltransferase WbdD

Structural highlights

4ax8 is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

WBDD_ECOLX Regulates the length of the LPS O-antigen polysaccharide chain. Stops the polymerization of the chain by phosphorylating and then methylating the phosphate on the terminal sugar. This terminal modification is essential for export of the O-antigen across the inner membrane. WbdD is also required for correct localization of the WbdA mannosyltransferase.^[1] ^[2] ^[3]

Publication Abstract from PubMed

WbdD is a bifunctional kinase/methyltransferase that is responsible for regulation of lipopolysaccharide O antigen polysaccharide chain length in Escherichia coli serotype O9a. Solving the crystal structure of this protein proved to be a challenge because the available crystals belonging to space group I23 only diffracted to low resolution (>95% of the crystals diffracted to resolution lower than 4 A and most only to 8 A) and were non-isomorphous, with changes in unit-cell dimensions of greater than 10%. Data from a serendipitously found single native crystal that diffracted to 3.0 A resolution were non-isomorphous with a lower (3.5 A) resolution selenomethionine data set. Here, a strategy for improving poor (3.5 A resolution) initial phases by density modification and cross-crystal averaging with an additional 4.2 A resolution data set to build a crude model of WbdD is desribed. Using this crude model as a mask to cut out the 3.5 A resolution electron density yielded a successful molecular-replacement solution of the 3.0 A resolution data set. The resulting map was used to build a complete model of WbdD. The hydration status of individual crystals appears to underpin the variable diffraction quality of WbdD crystals. After the initial structure had been solved, methods to control the hydration status of WbdD were developed and it was thus possible to routinely obtain high-resolution diffraction (to better than 2.5 A resolution). This novel and facile crystal-dehydration protocol may be useful for similar challenging situations.

Crystallization, dehydration and experimental phasing of WbdD, a bifunctional kinase and methyltransferase from Escherichia coli O9a.,Hagelueken G, Huang H, Harlos K, Clarke BR, Whitfield C, Naismith JH Acta Crystallogr D Biol Crystallogr. 2012 Oct;68(Pt 10):1371-9. Epub 2012 Sep 18. PMID:22993091^[4]

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

References

↑ Clarke BR, Cuthbertson L, Whitfield C. Nonreducing terminal modifications determine the chain length of polymannose O antigens of Escherichia coli and couple chain termination to polymer export via an ATP-binding cassette transporter. J Biol Chem. 2004 Aug 20;279(34):35709-18. PMID:15184370 doi:10.1074/jbc.M404738200
↑ Clarke BR, Greenfield LK, Bouwman C, Whitfield C. Coordination of polymerization, chain termination, and export in assembly of the Escherichia coli lipopolysaccharide O9a antigen in an ATP-binding cassette transporter-dependent pathway. J Biol Chem. 2009 Oct 30;284(44):30662-72. PMID:19734145 doi:10.1074/jbc.M109.052878
↑ Clarke BR, Richards MR, Greenfield LK, Hou D, Lowary TL, Whitfield C. In vitro reconstruction of the chain termination reaction in biosynthesis of the Escherichia coli O9a O-polysaccharide: the chain-length regulator, WbdD, catalyzes the addition of methyl phosphate to the non-reducing terminus of the growing glycan. J Biol Chem. 2011 Dec 2;286(48):41391-41401. PMID:21990359 doi:10.1074/jbc.M111.295857
↑ Hagelueken G, Huang H, Harlos K, Clarke BR, Whitfield C, Naismith JH. Crystallization, dehydration and experimental phasing of WbdD, a bifunctional kinase and methyltransferase from Escherichia coli O9a. Acta Crystallogr D Biol Crystallogr. 2012 Oct;68(Pt 10):1371-9. Epub 2012 Sep 18. PMID:22993091 doi:http://dx.doi.org/10.1107/S0907444912029599

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/4ax8"

Categories: Escherichia coli | Large Structures | Hagelueken G | Huang H | Naismith JH

@@ Line 1: / Line 1: @@
 ==Medium resolution structure of the bifunctional kinase- methyltransferase WbdD==
-<StructureSection load='4ax8' size='340' side='right' caption='[[4ax8]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='4ax8' size='340' side='right'caption='[[4ax8]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ax8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AX8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AX8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ax8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AX8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AX8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4azs|4azs]], [[4azt|4azt]], [[4azv|4azv]], [[4azw|4azw]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4ax8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ax8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ax8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ax8 PDBsum]</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=4ax8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ax8 OCA], [https://pdbe.org/4ax8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ax8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ax8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ax8 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/WBDD_ECOLX WBDD_ECOLX] Regulates the length of the LPS O-antigen polysaccharide chain. Stops the polymerization of the chain by phosphorylating and then methylating the phosphate on the terminal sugar. This terminal modification is essential for export of the O-antigen across the inner membrane. WbdD is also required for correct localization of the WbdA mannosyltransferase.<ref>PMID:15184370</ref> <ref>PMID:19734145</ref> <ref>PMID:21990359</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 15: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4ax8" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 20: / Line 24: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Hagelueken, G]]
+[[Category: Large Structures]]
-[[Category: Huang, H]]
+[[Category: Hagelueken G]]
-[[Category: Naismith, J H]]
+[[Category: Huang H]]
-[[Category: Kinase]]
+[[Category: Naismith JH]]
-[[Category: Methyltransferase]]
-[[Category: Transferase]]

4ax8

From Proteopedia

Current revision

Medium resolution structure of the bifunctional kinase- methyltransferase WbdD

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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