4m7s: Difference between revisions

Revision as of 11:01, 21 December 2022

Crystal structure of SeMet BtrN in an OPEN conformation

Structural highlights

4m7s is a 1 chain structure with sequence from Niallia circulans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	GOL, IMD, MSE, SF4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BTRN_NIACI Catalyzes the radical S-adenosyl-L-methionine (SAM)-dependent two-electron oxidation of 2-deoxy-scyllo-inosamine (DOIA) to amino-dideoxy-scyllo-inosose (amino-DOI) in the biosynthetic pathway of butirosin.^[1]

Publication Abstract from PubMed

The 2-deoxy-scyllo-inosamine (DOIA) dehydrogenases are key enzymes in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics. In contrast to most DOIA dehydrogenases, which are NAD-dependent, the DOIA dehydrogenase from Bacillus circulans (BtrN) is an S-adenosyl-l-methionine (AdoMet) radical enzyme. To examine how BtrN employs AdoMet radical chemistry, we have determined its structure with AdoMet and substrate to 1.56 A resolution. We find a previously undescribed modification to the core AdoMet radical fold: instead of the canonical (beta/alpha)6 architecture, BtrN displays a (beta5/alpha4) motif. We further find that an auxiliary [4Fe-4S] cluster in BtrN, thought to bind substrate, is instead implicated in substrate-radical oxidation. High structural homology in the auxiliary cluster binding region between BtrN, fellow AdoMet radical dehydrogenase anSME, and molybdenum cofactor biosynthetic enzyme MoaA provides support for the establishment of an AdoMet radical structural motif that is likely common to approximately 6,400 uncharacterized AdoMet radical enzymes.

X-ray analysis of butirosin biosynthetic enzyme BtrN redefines structural motifs for AdoMet radical chemistry.,Goldman PJ, Grove TL, Booker SJ, Drennan CL Proc Natl Acad Sci U S A. 2013 Sep 18. PMID:24048029^[2]

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

References

↑ Yokoyama K, Numakura M, Kudo F, Ohmori D, Eguchi T. Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin. J Am Chem Soc. 2007 Dec 12;129(49):15147-55. doi: 10.1021/ja072481t. Epub 2007 , Nov 15. PMID:18001019 doi:https://dx.doi.org/10.1021/ja072481t
↑ Goldman PJ, Grove TL, Booker SJ, Drennan CL. X-ray analysis of butirosin biosynthetic enzyme BtrN redefines structural motifs for AdoMet radical chemistry. Proc Natl Acad Sci U S A. 2013 Sep 18. PMID:24048029 doi:10.1073/pnas.1312228110

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Yokoyama K, Numakura M, Kudo F, Ohmori D, Eguchi T. Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin. J Am Chem Soc. 2007 Dec 12;129(49):15147-55. doi: 10.1021/ja072481t. Epub 2007 , Nov 15. PMID:18001019 doi:https://dx.doi.org/10.1021/ja072481t

[2] Goldman PJ, Grove TL, Booker SJ, Drennan CL. X-ray analysis of butirosin biosynthetic enzyme BtrN redefines structural motifs for AdoMet radical chemistry. Proc Natl Acad Sci U S A. 2013 Sep 18. PMID:24048029 doi:10.1073/pnas.1312228110

[1]

[2]

@@ Line 1: / Line 1: @@
 ==Crystal structure of SeMet BtrN in an OPEN conformation==
-<StructureSection load='4m7s' size='340' side='right' caption='[[4m7s]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
+<StructureSection load='4m7s' size='340' side='right'caption='[[4m7s]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4m7s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_24 Atcc 24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M7S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M7S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4m7s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Niallia_circulans Niallia circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M7S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M7S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</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=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=4m7s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m7s OCA], [https://pdbe.org/4m7s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m7s RCSB], [https://www.ebi.ac.uk/pdbsum/4m7s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m7s ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4m7t|4m7t]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">btrN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1397 ATCC 24])</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=4m7s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m7s OCA], [http://pdbe.org/4m7s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4m7s RCSB], [http://www.ebi.ac.uk/pdbsum/4m7s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4m7s ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/BTRN_NIACI BTRN_NIACI] Catalyzes the radical S-adenosyl-L-methionine (SAM)-dependent two-electron oxidation of 2-deoxy-scyllo-inosamine (DOIA) to amino-dideoxy-scyllo-inosose (amino-DOI) in the biosynthetic pathway of butirosin.<ref>PMID:18001019</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 24]]
+[[Category: Large Structures]]
-[[Category: Drennan, C L]]
+[[Category: Niallia circulans]]
-[[Category: Goldman, P J]]
+[[Category: Drennan CL]]
-[[Category: Adomet radical fold]]
+[[Category: Goldman PJ]]
-[[Category: Metal binding protein]]

4m7s: Difference between revisions

Revision as of 11:01, 21 December 2022

Crystal structure of SeMet BtrN in an OPEN conformation

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools