4kmi: Difference between revisions

Revision as of 08:59, 7 December 2022

Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with PO4

Structural highlights

4kmi is a 2 chain structure with sequence from Bacteroides fragilis NCTC 9343. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	MPD, PO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MGP_BACFN Converts 4-O-beta-D-mannopyranosyl-D-glucopyranose (Man-Glc) to mannose 1-phosphate (Man1P) and glucose. Involved in a mannan catabolic pathway which feeds into glycolysis.^[1]

Publication Abstract from PubMed

The crystal structure of a novel component of the mannan biodegradation system, 4-O-beta-d-mannosyl-d-glucose phosphorylase (MGP), was determined to a 1.68-A resolution. The structure of the enzyme revealed a unique homohexameric structure, which was formed by using two helices attached to the N-terminus and C-terminus as a tab for sticking between subunits. The structures of MGP complexes with genuine substrates, 4-O-beta-d-mannosyl-d-glucose and phosphate, and the product d-mannose-1-phosphate were also determined. The complex structures revealed that the invariant residue Asp131, which is supposed to be the general acid/base, did not exist close to the glycosidic Glc-O4 atom, which should be protonated in the catalytic reaction. Also, no solvent molecule that might mediate a proton transfer from Asp131 was observed in the substrate complex structure, suggesting that the catalytic mechanism of MGP is different from those of known disaccharide phosphorylases.

Structure of Novel Enzyme in Mannan Biodegradation Process 4-O-beta-d-Mannosyl-d-Glucose Phosphorylase MGP.,Nakae S, Ito S, Higa M, Senoura T, Wasaki J, Hijikata A, Shionyu M, Ito S, Shirai T J Mol Biol. 2013 Aug 14. pii: S0022-2836(13)00505-6. doi:, 10.1016/j.jmb.2013.08.002. PMID:23954514^[2]

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

References

↑ Senoura T, Ito S, Taguchi H, Higa M, Hamada S, Matsui H, Ozawa T, Jin S, Watanabe J, Wasaki J, Ito S. New microbial mannan catabolic pathway that involves a novel mannosylglucose phosphorylase. Biochem Biophys Res Commun. 2011 May 20;408(4):701-6. doi:, 10.1016/j.bbrc.2011.04.095. Epub 2011 Apr 24. PMID:21539815 doi:10.1016/j.bbrc.2011.04.095
↑ Nakae S, Ito S, Higa M, Senoura T, Wasaki J, Hijikata A, Shionyu M, Ito S, Shirai T. Structure of Novel Enzyme in Mannan Biodegradation Process 4-O-beta-d-Mannosyl-d-Glucose Phosphorylase MGP. J Mol Biol. 2013 Aug 14. pii: S0022-2836(13)00505-6. doi:, 10.1016/j.jmb.2013.08.002. PMID:23954514 doi:10.1016/j.jmb.2013.08.002

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Senoura T, Ito S, Taguchi H, Higa M, Hamada S, Matsui H, Ozawa T, Jin S, Watanabe J, Wasaki J, Ito S. New microbial mannan catabolic pathway that involves a novel mannosylglucose phosphorylase. Biochem Biophys Res Commun. 2011 May 20;408(4):701-6. doi:, 10.1016/j.bbrc.2011.04.095. Epub 2011 Apr 24. PMID:21539815 doi:10.1016/j.bbrc.2011.04.095

[2] Nakae S, Ito S, Higa M, Senoura T, Wasaki J, Hijikata A, Shionyu M, Ito S, Shirai T. Structure of Novel Enzyme in Mannan Biodegradation Process 4-O-beta-d-Mannosyl-d-Glucose Phosphorylase MGP. J Mol Biol. 2013 Aug 14. pii: S0022-2836(13)00505-6. doi:, 10.1016/j.jmb.2013.08.002. PMID:23954514 doi:10.1016/j.jmb.2013.08.002

[1]

[2]

@@ Line 1: / Line 1: @@
 ==Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with PO4==
-<StructureSection load='4kmi' size='340' side='right' caption='[[4kmi]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='4kmi' size='340' side='right'caption='[[4kmi]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4kmi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacfn Bacfn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KMI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4kmi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_fragilis_NCTC_9343 Bacteroides fragilis NCTC 9343]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KMI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3was|3was]], [[3wat|3wat]], [[3wau|3wau]]</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=4kmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmi OCA], [https://pdbe.org/4kmi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kmi RCSB], [https://www.ebi.ac.uk/pdbsum/4kmi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kmi ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BF0772 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272559 BACFN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-O-beta-D-mannosyl-D-glucose_phosphorylase 4-O-beta-D-mannosyl-D-glucose phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.281 2.4.1.281] </span></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=4kmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmi OCA], [http://pdbe.org/4kmi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kmi RCSB], [http://www.ebi.ac.uk/pdbsum/4kmi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kmi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MGP_BACFN MGP_BACFN]] Converts 4-O-beta-D-mannopyranosyl-D-glucopyranose (Man-Glc) to mannose 1-phosphate (Man1P) and glucose. Involved in a mannan catabolic pathway which feeds into glycolysis.<ref>PMID:21539815</ref>
+[https://www.uniprot.org/uniprot/MGP_BACFN MGP_BACFN] Converts 4-O-beta-D-mannopyranosyl-D-glucopyranose (Man-Glc) to mannose 1-phosphate (Man1P) and glucose. Involved in a mannan catabolic pathway which feeds into glycolysis.<ref>PMID:21539815</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: 4-O-beta-D-mannosyl-D-glucose phosphorylase]]
+[[Category: Bacteroides fragilis NCTC 9343]]
-[[Category: Bacfn]]
+[[Category: Large Structures]]
-[[Category: Higa, M]]
+[[Category: Higa M]]
-[[Category: Hijikata, A]]
+[[Category: Hijikata A]]
-[[Category: Ito, S]]
+[[Category: Ito S]]
-[[Category: Nakae, S]]
+[[Category: Nakae S]]
-[[Category: Senoura, T]]
+[[Category: Senoura T]]
-[[Category: Shionyu, M]]
+[[Category: Shionyu M]]
-[[Category: Shirai, T]]
+[[Category: Shirai T]]
-[[Category: Wasaki, J]]
+[[Category: Wasaki J]]
-[[Category: 5-bladed beta propeller fold]]
-[[Category: Mannan biodegradation]]
-[[Category: Phosphorylase]]
-[[Category: Transferase]]

4kmi: Difference between revisions

Revision as of 08:59, 7 December 2022

Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with PO4

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