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1x1j

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Crystal Structure of Xanthan Lyase (N194A) with a Substrate.

Structural highlights

1x1j is a 1 chain structure with sequence from Bacillus sp. GL1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XANLY_BACGL Plays a role in xanthan depolymerization pathway by cleaving the linkage between the terminal mannosyl and glucuronyl residues of the side chain of xanthan to liberate pyruvylated mannose.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Bacillus sp. GL1 xanthan lyase, a member of polysaccharide lyase family 8 (PL-8), acts exolytically on the side-chains of pentasaccharide-repeating polysaccharide xanthan and cleaves the glycosidic bond between glucuronic acid (GlcUA) and pyruvylated mannose (PyrMan) through a beta-elimination reaction. To clarify the enzyme reaction mechanism, i.e. its substrate recognition and catalytic reaction, we determined crystal structures of a mutant enzyme, N194A, in complexes with the product (PyrMan) and a substrate (pentasacharide) and in a ligand-free form at 1.8, 2.1, and 2.3A resolution. Based on the structures of the mutant in complexes with the product and substrate, we found that xanthan lyase recognized the PyrMan residue at subsite -1 and the GlcUA residue at +1 on the xanthan side-chain and underwent little interaction with the main chain of the polysaccharide. The structure of the mutant-substrate complex also showed that the hydroxyl group of Tyr255 was close to both the C-5 atom of the GlcUA residue and the oxygen atom of the glycosidic bond to be cleaved, suggesting that Tyr255 likely acts as a general base that extracts the proton from C-5 of the GlcUA residue and as a general acid that donates the proton to the glycosidic bond. A structural comparison of catalytic centers of PL-8 lyases indicated that the catalytic reaction mechanism is shared by all members of the family PL-8, while the substrate recognition mechanism differs.

Crystal structure of Bacillus sp. GL1 xanthan lyase complexed with a substrate: insights into the enzyme reaction mechanism.,Maruyama Y, Hashimoto W, Mikami B, Murata K J Mol Biol. 2005 Jul 29;350(5):974-86. PMID:15979090^[4]

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

References

↑ Nankai H, Hashimoto W, Miki H, Kawai S, Murata K. Microbial system for polysaccharide depolymerization: enzymatic route for xanthan depolymerization by Bacillus sp. strain GL1. Appl Environ Microbiol. 1999 Jun;65(6):2520-6. PMID:10347037
↑ Hashimoto W, Miki H, Tsuchiya N, Nankai H, Murata K. Polysaccharide lyase: molecular cloning, sequencing, and overexpression of the xanthan lyase gene of Bacillus sp. strain GL1. Appl Environ Microbiol. 2001 Feb;67(2):713-20. PMID:11157235 doi:http://dx.doi.org/10.1128/AEM.67.2.713-720.2001
↑ Hashimoto W, Miki H, Tsuchiya N, Nankai H, Murata K. Xanthan lyase of Bacillus sp. strain GL1 liberates pyruvylated mannose from xanthan side chains. Appl Environ Microbiol. 1998 Oct;64(10):3765-8. PMID:9758797
↑ Maruyama Y, Hashimoto W, Mikami B, Murata K. Crystal structure of Bacillus sp. GL1 xanthan lyase complexed with a substrate: insights into the enzyme reaction mechanism. J Mol Biol. 2005 Jul 29;350(5):974-86. PMID:15979090 doi:10.1016/j.jmb.2005.05.055

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1x1j"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Xanthan Lyase (N194A) with a Substrate.==
-<StructureSection load='1x1j' size='340' side='right' caption='[[1x1j]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='1x1j' size='340' side='right'caption='[[1x1j]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1x1j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacgl Bacgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X1J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1x1j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._GL1 Bacillus sp. GL1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X1J FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=46D:(4AR,6R,7S,8R,8AR)-8-((5R,6R)-3-CARBOXY-TETRAHYDRO-4,5,6-TRIHYDROXY-2H-PYRAN-2-YLOXY)-HEXAHYDRO-6,7-DIHYDROXY-2-METHYLPYRANO[3,2-D][1,3]DIOXINE-2-CARBOXYLIC+ACID)'>46D</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1j0m|1j0m]], [[1j0n|1j0n]], [[1x1h|1x1h]], [[1x1i|1x1i]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=46D:(4AR,6R,7S,8R,8AR)-8-((5R,6R)-3-CARBOXY-TETRAHYDRO-4,5,6-TRIHYDROXY-2H-PYRAN-2-YLOXY)-HEXAHYDRO-6,7-DIHYDROXY-2-METHYLPYRANO[3,2-D][1,3]DIOXINE-2-CARBOXYLIC+ACID)'>46D</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </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=1x1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1j OCA], [https://pdbe.org/1x1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x1j RCSB], [https://www.ebi.ac.uk/pdbsum/1x1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x1j 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=1x1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1j OCA], [http://pdbe.org/1x1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x1j RCSB], [http://www.ebi.ac.uk/pdbsum/1x1j PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/XANLY_BACGL XANLY_BACGL] Plays a role in xanthan depolymerization pathway by cleaving the linkage between the terminal mannosyl and glucuronyl residues of the side chain of xanthan to liberate pyruvylated mannose.<ref>PMID:10347037</ref> <ref>PMID:11157235</ref> <ref>PMID:9758797</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x1/1x1j_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x1/1x1j_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bacgl]]
+[[Category: Bacillus sp. GL1]]
-[[Category: Xanthan lyase]]
+[[Category: Large Structures]]
-[[Category: Hashimoto, W]]
+[[Category: Hashimoto W]]
-[[Category: Maruyama, Y]]
+[[Category: Maruyama Y]]
-[[Category: Mikami, B]]
+[[Category: Mikami B]]
-[[Category: Murata, K]]
+[[Category: Murata K]]
-[[Category: Alpha/alpha barrel]]
-[[Category: Beta sandwich]]
-[[Category: Lyase]]

1x1j

From Proteopedia

Current revision

Crystal Structure of Xanthan Lyase (N194A) with a Substrate.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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