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5k7p

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Revision as of 09:25, 1 July 2020

MicroED structure of xylanase at 2.3 A resolution

Structural highlights

5k7p is a 1 chain structure with sequence from Hypocrea jecorina. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	5k7n, 5k7o, 5k7q, 5k7r, 5k7s, 5k7t
Activity:	Endo-1,4-beta-xylanase, with EC number 3.2.1.8
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[XYN2_HYPJR] Glycoside hydrolase involved in the hydrolysis of xylan, a major plant cell wall hemicellulose made up of 1,4-beta-linked D-xylopyranose residues. Catalyzes the endohydrolysis of the main-chain 1,4-beta-glycosidic bonds connecting the xylose subunits yielding various xylooligosaccharides and xylose (PubMed:1369024, Ref.5). The catalysis proceeds by a double-displacement reaction mechanism with a putative covalent glycosyl-enzyme intermediate, with retention of the anomeric configuration (PubMed:7988708). Produces xylobiose and xylose as the main degradation products (PubMed:19556747).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.

Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.,de la Cruz MJ, Hattne J, Shi D, Seidler P, Rodriguez J, Reyes FE, Sawaya MR, Cascio D, Weiss SC, Kim SK, Hinck CS, Hinck AP, Calero G, Eisenberg D, Gonen T Nat Methods. 2017 Feb 13;14(4):399-402. doi: 10.1038/nmeth.4178. PMID:28192420^[5]

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

References

↑ Torronen A, Mach RL, Messner R, Gonzalez R, Kalkkinen N, Harkki A, Kubicek CP. The two major xylanases from Trichoderma reesei: characterization of both enzymes and genes. Biotechnology (N Y). 1992 Nov;10(11):1461-5. PMID:1369024
↑ Jun H, Bing Y, Keying Z, Xuemei D, Daiwen C. Sequencing and expression of the xylanase gene 2 from Trichoderma reesei Rut C-30 and characterization of the recombinant enzyme and its activity on xylan. J Mol Microbiol Biotechnol. 2009;17(3):101-9. doi: 10.1159/000226590. Epub 2009, Jun 26. PMID:19556747 doi:http://dx.doi.org/10.1159/000226590
↑ Biely P, Kremnicky L, Alfoldi J, Tenkanen M. Stereochemistry of the hydrolysis of glycosidic linkage by endo-beta-1,4-xylanases of Trichoderma reesei. FEBS Lett. 1994 Dec 12;356(1):137-40. PMID:7988708
↑ Torronen A, Mach RL, Messner R, Gonzalez R, Kalkkinen N, Harkki A, Kubicek CP. The two major xylanases from Trichoderma reesei: characterization of both enzymes and genes. Biotechnology (N Y). 1992 Nov;10(11):1461-5. PMID:1369024
↑ de la Cruz MJ, Hattne J, Shi D, Seidler P, Rodriguez J, Reyes FE, Sawaya MR, Cascio D, Weiss SC, Kim SK, Hinck CS, Hinck AP, Calero G, Eisenberg D, Gonen T. Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED. Nat Methods. 2017 Feb 13;14(4):399-402. doi: 10.1038/nmeth.4178. PMID:28192420 doi:http://dx.doi.org/10.1038/nmeth.4178

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/5k7p"

@@ Line 1: / Line 1: @@
 ==MicroED structure of xylanase at 2.3 A resolution==
-<StructureSection load='5k7p' size='340' side='right' caption='[[5k7p]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='5k7p' size='340' side='right'caption='[[5k7p]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5k7p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K7P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5k7p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K7P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K7P FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k7n|5k7n]], [[5k7o|5k7o]], [[5k7q|5k7q]], [[5k7r|5k7r]], [[5k7s|5k7s]], [[5k7t|5k7t]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=5k7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k7p OCA], [http://pdbe.org/5k7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k7p RCSB], [http://www.ebi.ac.uk/pdbsum/5k7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k7p ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5k7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k7p OCA], [http://pdbe.org/5k7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k7p RCSB], [http://www.ebi.ac.uk/pdbsum/5k7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k7p ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 26: / Line 26: @@
 [[Category: Endo-1,4-beta-xylanase]]
 [[Category: Hypocrea jecorina]]
+[[Category: Large Structures]]
 [[Category: Cascio, D]]
 [[Category: Cruz, M J.de la]]

5k7p

From Proteopedia

Revision as of 09:25, 1 July 2020

MicroED structure of xylanase at 2.3 A resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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