4cd4: Difference between revisions

Latest revision as of 12:08, 20 December 2023

The structure of GH26 beta-mannanase CjMan26C from Cellvibrio japonicus in complex with ManIFG

Structural highlights

4cd4 is a 1 chain structure with sequence from Cellvibrio japonicus Ueda107. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.2Å
Ligands:	BMA, IFM, NA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B3PGI1_CELJU

Publication Abstract from PubMed

Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including beta-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar-shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition.

Combined inhibitor free-energy landscape and structural analysis reports on the mannosidase conformational coordinate.,Williams RJ, Iglesias-Fernandez J, Stepper J, Jackson A, Thompson AJ, Lowe EC, White JM, Gilbert HJ, Rovira C, Davies GJ, Williams SJ Angew Chem Int Ed Engl. 2014 Jan 20;53(4):1087-91. doi: 10.1002/anie.201308334., Epub 2013 Dec 11. PMID:24339341^[1]

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

References

↑ Williams RJ, Iglesias-Fernandez J, Stepper J, Jackson A, Thompson AJ, Lowe EC, White JM, Gilbert HJ, Rovira C, Davies GJ, Williams SJ. Combined inhibitor free-energy landscape and structural analysis reports on the mannosidase conformational coordinate. Angew Chem Int Ed Engl. 2014 Jan 20;53(4):1087-91. doi: 10.1002/anie.201308334., Epub 2013 Dec 11. PMID:24339341 doi:https://dx.doi.org/10.1002/anie.201308334

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OCA

[1] Williams RJ, Iglesias-Fernandez J, Stepper J, Jackson A, Thompson AJ, Lowe EC, White JM, Gilbert HJ, Rovira C, Davies GJ, Williams SJ. Combined inhibitor free-energy landscape and structural analysis reports on the mannosidase conformational coordinate. Angew Chem Int Ed Engl. 2014 Jan 20;53(4):1087-91. doi: 10.1002/anie.201308334., Epub 2013 Dec 11. PMID:24339341 doi:https://dx.doi.org/10.1002/anie.201308334

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='4cd4' size='340' side='right'caption='[[4cd4]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4cd4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Celju Celju]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CD4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CD4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4cd4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus_Ueda107 Cellvibrio japonicus Ueda107]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CD4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=IFM:5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE'>IFM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4cd5|4cd5]], [[4cd6|4cd6]], [[4cd7|4cd7]], [[4cd8|4cd8]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=IFM:5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE'>IFM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannan_endo-1,4-beta-mannosidase Mannan endo-1,4-beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.78 3.2.1.78] </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=4cd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cd4 OCA], [https://pdbe.org/4cd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cd4 RCSB], [https://www.ebi.ac.uk/pdbsum/4cd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cd4 ProSAT]</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=4cd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cd4 OCA], [http://pdbe.org/4cd4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4cd4 RCSB], [http://www.ebi.ac.uk/pdbsum/4cd4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4cd4 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/B3PGI1_CELJU B3PGI1_CELJU]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Celju]]
+[[Category: Cellvibrio japonicus Ueda107]]
 [[Category: Large Structures]]
-[[Category: Mannan endo-1,4-beta-mannosidase]]
+[[Category: Davies GJ]]
-[[Category: Davies, G J]]
+[[Category: Gilbert HJ]]
-[[Category: Gilbert, H J]]
+[[Category: Iglesias-Fernandez J]]
-[[Category: Iglesias-Fernandez, J]]
+[[Category: Jackson A]]
-[[Category: Jackson, A]]
+[[Category: Lowe EC]]
-[[Category: Lowe, E C]]
+[[Category: Rovira C]]
-[[Category: Rovira, C]]
+[[Category: Stepper J]]
-[[Category: Stepper, J]]
+[[Category: Thompson AJ]]
-[[Category: Thompson, A J]]
+[[Category: White JM]]
-[[Category: White, J M]]
+[[Category: Williams RJ]]
-[[Category: Williams, R J]]
+[[Category: Williams SJ]]
-[[Category: Williams, S J]]
-[[Category: Beta-mannosidase]]
-[[Category: Biocatalysis]]
-[[Category: Cazy]]
-[[Category: Conformation]]
-[[Category: Enzyme-carbohydrate interaction]]
-[[Category: Gh113]]
-[[Category: Gh26]]
-[[Category: Glycosidase inhibition]]
-[[Category: Glycoside hydrolase]]
-[[Category: Hydrolase]]
-[[Category: Mannose]]
-[[Category: Mannosidase]]
-[[Category: Quantum mechanic]]

4cd4: Difference between revisions

Latest revision as of 12:08, 20 December 2023

The structure of GH26 beta-mannanase CjMan26C from Cellvibrio japonicus in complex with ManIFG

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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