1uv4

From Proteopedia

(Difference between revisions)

Current revision

Native Bacillus subtilis Arabinanase Arb43A

Structural highlights

1uv4 is a 1 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EABN1_BACSU Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of linear 1,5-alpha-L-arabinan and of branched sugar beet arabinan. It displays no activity against heavily substituted arabinans or a range of other polysaccharides (larch wood arabinogalactan, wheat arabinoxylan and p-nitrophenyl-alpha-L-arabinofuranoside). The enzyme activity is progressively reduced as alpha-(1->5)-chains become shorter or more highly substituted.^[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

Enzymes acting on polymeric substrates are frequently classified as exo or endo, reflecting their preference for, or ignorance of, polymer chain ends. Most biotechnological applications, especially in the field of polysaccharide degradation, require either endo- or exo-acting hydrolases, or they harness the essential synergy between these two modes of action. Here, we have used genomic data in tandem with structure to modify, radically, the chain-end specificity of the Cellvibrio japonicus exo-arabinanase CjArb43A. The structure of Bacillus subtilis endo-arabinanase 43A (BsArb43A) in harness with chain-end recognition kinetics of CjArb43A directed a rational design approach that led to the conversion of the Cellvibrio enzyme from an exo to an endo mode of action. One of the exo-acting mutants, D35L/Q316A, displays similar activity to WT CjArb43A and the removal of the steric block mediated by the side chains of Gln-316 and Asp-53 at the -3 subsite confers its capacity to attack internal glycoside bonds. This study provides a template for the production of tailored industrial catalysts. The introduction of subtle changes informed by comparative 3D structural and genomic data can lead to fundamental changes in the mode of action of these enzymes.

Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A.,Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, Gilbert HJ Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2697-702. Epub 2005 Feb 11. PMID:15708971^[4]

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

References

↑ Raposo MP, Inacio JM, Mota LJ, de Sa-Nogueira I. Transcriptional regulation of genes encoding arabinan-degrading enzymes in Bacillus subtilis. J Bacteriol. 2004 Mar;186(5):1287-96. PMID:14973026
↑ Leal TF, de Sa-Nogueira I. Purification, characterization and functional analysis of an endo-arabinanase (AbnA) from Bacillus subtilis. FEMS Microbiol Lett. 2004 Dec 1;241(1):41-8. PMID:15556708 doi:http://dx.doi.org/S0378-1097(04)00721-9
↑ Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, Gilbert HJ. Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A. Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2697-702. Epub 2005 Feb 11. PMID:15708971
↑ Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, Gilbert HJ. Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A. Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2697-702. Epub 2005 Feb 11. PMID:15708971

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1uv4"

@@ Line 1: / Line 1: @@
-[[Image:1uv4.gif|left|200px]]<br />
-<applet load="1uv4" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1uv4, resolution 1.50&Aring;" />
-'''NATIVE BACILLUS SUBTILIS ARABINANASE ARB43A'''<br />
-==Overview==
+==Native Bacillus subtilis Arabinanase Arb43A==
-Enzymes acting on polymeric substrates are frequently classified as exo or, endo, reflecting their preference for, or ignorance of, polymer chain, ends. Most biotechnological applications, especially in the field of, polysaccharide degradation, require either endo- or exo-acting hydrolases, or they harness the essential synergy between these two modes of action., Here, we have used genomic data in tandem with structure to modify, radically, the chain-end specificity of the Cellvibrio japonicus, exo-arabinanase CjArb43A. The structure of Bacillus subtilis, endo-arabinanase 43A (BsArb43A) in harness with chain-end recognition, kinetics of CjArb43A directed a rational design approach that led to the, conversion of the Cellvibrio enzyme from an exo to an endo mode of action., One of the ... [[http://ispc.weizmann.ac.il/pmbin/getpm?15708971 (full description)]]
+<StructureSection load='1uv4' size='340' side='right'caption='[[1uv4]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1uv4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UV4 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=1uv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uv4 OCA], [https://pdbe.org/1uv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uv4 RCSB], [https://www.ebi.ac.uk/pdbsum/1uv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uv4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/EABN1_BACSU EABN1_BACSU] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of linear 1,5-alpha-L-arabinan and of branched sugar beet arabinan. It displays no activity against heavily substituted arabinans or a range of other polysaccharides (larch wood arabinogalactan, wheat arabinoxylan and p-nitrophenyl-alpha-L-arabinofuranoside). The enzyme activity is progressively reduced as alpha-(1->5)-chains become shorter or more highly substituted.<ref>PMID:14973026</ref> <ref>PMID:15556708</ref> <ref>PMID:15708971</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/uv/1uv4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=1uv4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Enzymes acting on polymeric substrates are frequently classified as exo or endo, reflecting their preference for, or ignorance of, polymer chain ends. Most biotechnological applications, especially in the field of polysaccharide degradation, require either endo- or exo-acting hydrolases, or they harness the essential synergy between these two modes of action. Here, we have used genomic data in tandem with structure to modify, radically, the chain-end specificity of the Cellvibrio japonicus exo-arabinanase CjArb43A. The structure of Bacillus subtilis endo-arabinanase 43A (BsArb43A) in harness with chain-end recognition kinetics of CjArb43A directed a rational design approach that led to the conversion of the Cellvibrio enzyme from an exo to an endo mode of action. One of the exo-acting mutants, D35L/Q316A, displays similar activity to WT CjArb43A and the removal of the steric block mediated by the side chains of Gln-316 and Asp-53 at the -3 subsite confers its capacity to attack internal glycoside bonds. This study provides a template for the production of tailored industrial catalysts. The introduction of subtle changes informed by comparative 3D structural and genomic data can lead to fundamental changes in the mode of action of these enzymes.
-==About this Structure==
+Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A.,Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, Gilbert HJ Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2697-702. Epub 2005 Feb 11. PMID:15708971<ref>PMID:15708971</ref>
-UV4 is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]] with CA and EDO as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/ ]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.99 3.2.1.99]]. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UV4 OCA]].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A., Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, Gilbert HJ, Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2697-702. Epub 2005 Feb 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15708971 15708971]
+</div>
-[[Category: Bacillus subtilis]]
+<div class="pdbe-citations 1uv4" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
-[[Category: Davies, G.J.]]
-[[Category: Gilbert, H.J.]]
-[[Category: Nurizzo, D.]]
-[[Category: Taylor, E.J.]]
-[[Category: CA]]
-[[Category: EDO]]
-[[Category: arabinase]]
-[[Category: bacillus]]
-[[Category: catalysis]]
-[[Category: hydrolase]]
-[[Category: propeller]]
-[[Category: subtilis]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Oct 29 20:15:43 2007''
+==See Also==
+*[[Arabinanase 3D structures|Arabinanase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bacillus subtilis]]
+[[Category: Large Structures]]
+[[Category: Davies GJ]]
+[[Category: Gilbert HJ]]
+[[Category: Nurizzo D]]
+[[Category: Taylor EJ]]

1uv4

From Proteopedia

Current revision

Native Bacillus subtilis Arabinanase Arb43A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox