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3ofk

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Revision as of 10:42, 18 May 2022

Crystal structure of N-methyltransferase NodS from Bradyrhizobium japonicum WM9 in complex with S-adenosyl-l-homocysteine (SAH)

Structural highlights

3ofk is a 4 chain structure with sequence from Brasw. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3ofj
Gene:	nodS (BRASW)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[Q9AQ22_BRASW] SAM-utilizing methyltransferase involved in nod factor synthesis.[PIRNR:PIRNR009310]

Publication Abstract from PubMed

NodS is an S-adenosyl-l-methionine (SAM)-dependent N-methyltransferase that is involved in the biosynthesis of Nod factor (NF) in rhizobia, which are bacterial symbionts of legume plants. NF is a modified chitooligosaccharide (COS) signal molecule that is recognized by the legume host, where it initiates symbiotic processes leading to atmospheric nitrogen fixation. We report the crystal structure of recombinant NodS protein from Bradyrhizobium japonicum, which infects lupine and serradella legumes. Two crystal forms-ligand-free NodS and NodS in complex with S-adenosyl-l-homocysteine, which is a by-product of the methylation reaction-were obtained, and their structures were refined to resolutions of 2.43 A and 1.85 A, respectively. Although the overall fold (consisting of a seven-stranded beta-sheet flanked by layers of helices) is similar to those of other SAM-dependent methyltransferases, NodS has specific features reflecting the unique character of its oligosaccharide substrate. In particular, the N-terminal helix and its connecting loop get ordered upon SAM binding, thereby closing the methyl donor cavity and shaping a long surface canyon that is clearly the binding site for the acceptor molecule. Comparison of the two structural forms of NodS suggests that there are also other conformational changes taking place upon the binding of the donor substrate. As an enzyme that methylates a COS substrate, NodS is the first example among all SAM-dependent methyltransferases to have its three-dimensional structure elucidated. Gaining insight about how NodS binds its donor and acceptor substrates helps to better understand the mechanism of NodS activity and the basis of its functional difference in various rhizobia.

Crystal Structures of NodS N-Methyltransferase from Bradyrhizobium japonicum in Ligand-Free Form and as SAH Complex.,Cakici O, Sikorski M, Stepkowski T, Bujacz G, Jaskolski M J Mol Biol. 2010 Oct 21. PMID:20970431^[1]

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

References

↑ Cakici O, Sikorski M, Stepkowski T, Bujacz G, Jaskolski M. Crystal Structures of NodS N-Methyltransferase from Bradyrhizobium japonicum in Ligand-Free Form and as SAH Complex. J Mol Biol. 2010 Oct 21. PMID:20970431 doi:10.1016/j.jmb.2010.10.016

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ofk"

@@ Line 1: / Line 1: @@
 ==Crystal structure of N-methyltransferase NodS from Bradyrhizobium japonicum WM9 in complex with S-adenosyl-l-homocysteine (SAH)==
-<StructureSection load='3ofk' size='340' side='right' caption='[[3ofk]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='3ofk' size='340' side='right'caption='[[3ofk]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ofk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Brasw Brasw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OFK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ofk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brasw Brasw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OFK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ofj|3ofj]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ofj|3ofj]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nodS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=133505 BRASW])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nodS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=133505 BRASW])</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=3ofk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ofk OCA], [http://pdbe.org/3ofk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ofk RCSB], [http://www.ebi.ac.uk/pdbsum/3ofk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ofk ProSAT]</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=3ofk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ofk OCA], [https://pdbe.org/3ofk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ofk RCSB], [https://www.ebi.ac.uk/pdbsum/3ofk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ofk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q9AQ22_BRASW Q9AQ22_BRASW]] SAM-utilizing methyltransferase involved in nod factor synthesis.[PIRNR:PIRNR009310]
+[[https://www.uniprot.org/uniprot/Q9AQ22_BRASW Q9AQ22_BRASW]] SAM-utilizing methyltransferase involved in nod factor synthesis.[PIRNR:PIRNR009310]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 28: @@
 </StructureSection>
 [[Category: Brasw]]
+[[Category: Large Structures]]
 [[Category: Bujacz, G]]
 [[Category: Cakici, O]]
@@ Line 38: / Line 39: @@
 [[Category: N-methyltransferase]]
 [[Category: Nitrogen fixation]]
-[[Category: Nod factor]]
 [[Category: Nod]]
+[[Category: Nod factor]]
 [[Category: Nodulation]]
 [[Category: Sah]]

3ofk

From Proteopedia

Revision as of 10:42, 18 May 2022

Crystal structure of N-methyltransferase NodS from Bradyrhizobium japonicum WM9 in complex with S-adenosyl-l-homocysteine (SAH)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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