1gye: Difference between revisions

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{{Seed}}
[[Image:1gye.png|left|200px]]


<!--
==Structure of Cellvibrio cellulosa alpha-L-arabinanase complexed with Arabinohexaose==
The line below this paragraph, containing "STRUCTURE_1gye", creates the "Structure Box" on the page.
<StructureSection load='1gye' size='340' side='right'caption='[[1gye]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1gye]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GYE FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
{{STRUCTURE_1gye|  PDB=1gye  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gye OCA], [https://pdbe.org/1gye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gye RCSB], [https://www.ebi.ac.uk/pdbsum/1gye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gye ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ARBA_CELJU ARBA_CELJU] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of the terminal alpha-(1->5)-arabinofuranosyl bonds of linear arabinan and carboxymethylarabinan to produce almost exclusively arabinotriose.<ref>PMID:12198486</ref> <ref>PMID:15708971</ref> <ref>PMID:9163351</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/gy/1gye_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=1gye ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cellvibrio japonicus arabinanase Arb43A hydrolyzes the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The three-dimensional structure of Arb43A, determined at 1.9 A resolution, reveals a five-bladed beta-propeller fold. Arb43A is the first enzyme known to display this topology. A long V-shaped surface groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. Three carboxylates deep in the active site groove provide the general acid and base components for glycosidic bond hydrolysis with inversion of anomeric configuration.


===STRUCTURE OF CELLVIBRIO CELLULOSA ALPHA-L-ARABINANASE COMPLEXED WITH ARABINOHEXAOSE===
Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold.,Nurizzo D, Turkenburg JP, Charnock SJ, Roberts SM, Dodson EJ, McKie VA, Taylor EJ, Gilbert HJ, Davies GJ Nat Struct Biol. 2002 Sep;9(9):665-8. PMID:12198486<ref>PMID:12198486</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1gye" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_12198486}}, adds the Publication Abstract to the page
*[[Arabinanase|Arabinanase]]
(as it appears on PubMed at http://www.pubmed.gov), where 12198486 is the PubMed ID number.
*[[Arabinanase 3D structures|Arabinanase 3D structures]]
-->
== References ==
{{ABSTRACT_PUBMED_12198486}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
1GYE is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYE OCA].
 
==Reference==
<ref group="xtra">PMID:12198486</ref><references group="xtra"/>
[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]
[[Category: Cellvibrio japonicus]]
[[Category: Cellvibrio japonicus]]
[[Category: Charnock, S J.]]
[[Category: Large Structures]]
[[Category: Davies, G J.]]
[[Category: Charnock SJ]]
[[Category: Dodson, E J.]]
[[Category: Davies GJ]]
[[Category: Gilbert, H J.]]
[[Category: Dodson EJ]]
[[Category: Mckie, V A.]]
[[Category: Gilbert HJ]]
[[Category: Nurizzo, D.]]
[[Category: McKie VA]]
[[Category: Roberts, S M.]]
[[Category: Nurizzo D]]
[[Category: Taylor, E J.]]
[[Category: Roberts SM]]
[[Category: Turkenburg, J P.]]
[[Category: Taylor EJ]]
[[Category: Arabinanase]]
[[Category: Turkenburg JP]]
[[Category: Catalysis]]
[[Category: Cellvibrio]]
[[Category: Hydrolase]]
[[Category: Propeller]]
[[Category: Pseudomona]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:18:37 2009''

Latest revision as of 11:28, 6 November 2024

Structure of Cellvibrio cellulosa alpha-L-arabinanase complexed with ArabinohexaoseStructure of Cellvibrio cellulosa alpha-L-arabinanase complexed with Arabinohexaose

Structural highlights

1gye is a 1 chain structure with sequence from Cellvibrio japonicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ARBA_CELJU Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of the terminal alpha-(1->5)-arabinofuranosyl bonds of linear arabinan and carboxymethylarabinan to produce almost exclusively arabinotriose.[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

Cellvibrio japonicus arabinanase Arb43A hydrolyzes the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The three-dimensional structure of Arb43A, determined at 1.9 A resolution, reveals a five-bladed beta-propeller fold. Arb43A is the first enzyme known to display this topology. A long V-shaped surface groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. Three carboxylates deep in the active site groove provide the general acid and base components for glycosidic bond hydrolysis with inversion of anomeric configuration.

Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold.,Nurizzo D, Turkenburg JP, Charnock SJ, Roberts SM, Dodson EJ, McKie VA, Taylor EJ, Gilbert HJ, Davies GJ Nat Struct Biol. 2002 Sep;9(9):665-8. PMID:12198486[4]

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

See Also

References

  1. ↑ Nurizzo D, Turkenburg JP, Charnock SJ, Roberts SM, Dodson EJ, McKie VA, Taylor EJ, Gilbert HJ, Davies GJ. Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold. Nat Struct Biol. 2002 Sep;9(9):665-8. PMID:12198486 doi:10.1038/nsb835
  2. ↑ 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
  3. ↑ McKie VA, Black GW, Millward-Sadler SJ, Hazlewood GP, Laurie JI, Gilbert HJ. Arabinanase A from Pseudomonas fluorescens subsp. cellulosa exhibits both an Biochem J. 1997 Apr 15;323 ( Pt 2)(Pt 2):547-55. PMID:9163351 doi:10.1042/bj3230547
  4. ↑ Nurizzo D, Turkenburg JP, Charnock SJ, Roberts SM, Dodson EJ, McKie VA, Taylor EJ, Gilbert HJ, Davies GJ. Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold. Nat Struct Biol. 2002 Sep;9(9):665-8. PMID:12198486 doi:10.1038/nsb835

1gye, resolution 2.50Å

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