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2e24

From Proteopedia

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Current revision

crystal structure of a mutant (R612A) of xanthan lyase

Structural highlights

2e24 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 2.15Å
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

Xanthan is a bacterial heteropolysaccharide composed of pentasaccharide repeating units, i.e., a cellobiose as a backbone and a trisaccharide consisting of two mannoses and one glucuronic acid as a side chain. Nonreducing terminal mannose residues of xanthan side chains are partially pyruvated. Bacillus sp. GL1 xanthan lyase, a member of polysaccharide lyase family 8, acts specifically on pyruvated side chains of xanthan and yields pyruvated mannose through a beta-elimination reaction by using a single Tyr255 residue as base and acid catalysts. Here we show structural factors for substrate recognition by xanthan lyase through X-ray crystallographic and mutational analyses. The enzyme accommodates mannose and pyruvated mannose at the -1 subsite, although both inhibitor and dissociation constants of the two monosaccharides indicated that the affinity of pyruvated mannose for xanthan lyase is much higher than that of mannose. The high affinity of pyruvated mannose is probably due to the formation of additional hydrogen bonds between the carboxyl group of pyruvated mannose and amino acid residues of Tyr315 and Arg612. Site-directed mutagenesis of the two residues demonstrated that Arg612 is a key residue in recognizing pyruvated mannose. Arg612 is located in the protruding loop covering the substrate, suggesting that the loop functions as a lid that is responsible for the proper accommodation of the substrate at the active site.

A structural factor responsible for substrate recognition by Bacillus sp. GL1 xanthan lyase that acts specifically on pyruvated side chains of xanthan.,Maruyama Y, Mikami B, Hashimoto W, Murata K Biochemistry. 2007 Jan 23;46(3):781-91. PMID:17223699^[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, Mikami B, Hashimoto W, Murata K. A structural factor responsible for substrate recognition by Bacillus sp. GL1 xanthan lyase that acts specifically on pyruvated side chains of xanthan. Biochemistry. 2007 Jan 23;46(3):781-91. PMID:17223699 doi:10.1021/bi0619775

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/2e24"

@@ Line 1: / Line 1: @@
 ==crystal structure of a mutant (R612A) of xanthan lyase==
-<StructureSection load='2e24' size='340' side='right' caption='[[2e24]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+<StructureSection load='2e24' size='340' side='right'caption='[[2e24]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2e24]] 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=2E24 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E24 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2e24]] 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=2E24 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E24 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.15&#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]], [[1x1j|1x1j]], [[2e22|2e22]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=2e24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e24 OCA], [https://pdbe.org/2e24 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e24 RCSB], [https://www.ebi.ac.uk/pdbsum/2e24 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e24 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=2e24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e24 OCA], [http://pdbe.org/2e24 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e24 RCSB], [http://www.ebi.ac.uk/pdbsum/2e24 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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/e2/2e24_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/2e24_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2e24 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 33: / 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: Lyase]]
-[[Category: Polysaccharide lyase]]
-[[Category: Xanthan]]

2e24

From Proteopedia

Current revision

crystal structure of a mutant (R612A) of xanthan lyase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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