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4xpv

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Neutron and X-ray structure analysis of xylanase: N44D at pH6

Structural highlights

4xpv is a 1 chain structure with sequence from Trichoderma reesei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Hybrid , Neutron Diffraction , X-ray diffraction, Resolution 1.7Å
Ligands:	,
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

Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.

Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.,Wan Q, Parks JM, Hanson BL, Fisher SZ, Ostermann A, Schrader TE, Graham DE, Coates L, Langan P, Kovalevsky A Proc Natl Acad Sci U S A. 2015 Sep 21. pii: 201504986. PMID:26392527^[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
↑ Wan Q, Parks JM, Hanson BL, Fisher SZ, Ostermann A, Schrader TE, Graham DE, Coates L, Langan P, Kovalevsky A. Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. Proc Natl Acad Sci U S A. 2015 Sep 21. pii: 201504986. PMID:26392527 doi:http://dx.doi.org/10.1073/pnas.1504986112

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/4xpv"

@@ Line 1: / Line 1: @@
 ==Neutron and X-ray structure analysis of xylanase: N44D at pH6==
-<StructureSection load='4xpv' size='340' side='right' caption='[[4xpv]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='4xpv' size='340' side='right'caption='[[4xpv]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xpv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XPV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xpv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XPV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></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=4xpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpv OCA], [http://pdbe.org/4xpv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xpv RCSB], [http://www.ebi.ac.uk/pdbsum/4xpv PDBsum]</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=4xpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpv OCA], [https://pdbe.org/4xpv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xpv RCSB], [https://www.ebi.ac.uk/pdbsum/4xpv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpv ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/XYN2_HYPJR 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).<ref>PMID:1369024</ref> <ref>PMID:19556747</ref> <ref>PMID:7988708</ref> <ref>PMID:1369024</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Endo-1,4-beta-xylanase]]
+[[Category: Large Structures]]
-[[Category: Coates, L]]
+[[Category: Trichoderma reesei]]
-[[Category: Fisher, Z]]
+[[Category: Coates L]]
-[[Category: Graham, D E]]
+[[Category: Fisher Z]]
-[[Category: Hanson, L B]]
+[[Category: Graham DE]]
-[[Category: Kovalevsky, A Y]]
+[[Category: Hanson LB]]
-[[Category: Langan, P]]
+[[Category: Kovalevsky AY]]
-[[Category: Ostermann, A]]
+[[Category: Langan P]]
-[[Category: Park, J M]]
+[[Category: Ostermann A]]
-[[Category: Riccardi, D M]]
+[[Category: Park JM]]
-[[Category: Schrader, T]]
+[[Category: Riccardi DM]]
-[[Category: Smith, J C]]
+[[Category: Schrader T]]
-[[Category: Wan, Q]]
+[[Category: Smith JC]]
-[[Category: Hydrolase]]
+[[Category: Wan Q]]
-[[Category: Jelly roll]]

4xpv

From Proteopedia

Current revision

Neutron and X-ray structure analysis of xylanase: N44D at pH6

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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