1gyh

From Proteopedia

(Difference between revisions)

Current revision

Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant

Structural highlights

1gyh is a 6 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 1.89Å
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.

References

↑ 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
↑ 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
↑ 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
↑ 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

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/1gyh"

@@ Line 1: / Line 1: @@
-[[Image:1gyh.jpg|left|200px]]
-<!--
+==Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant==
-The line below this paragraph, containing "STRUCTURE_1gyh", creates the "Structure Box" on the page.
+<StructureSection load='1gyh' size='340' side='right'caption='[[1gyh]], [[Resolution|resolution]] 1.89&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'>[[1gyh]] is a 6 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=1GYH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GYH 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]] 1.89&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-{{STRUCTURE_1gyh|  PDB=1gyh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyh OCA], [https://pdbe.org/1gyh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gyh RCSB], [https://www.ebi.ac.uk/pdbsum/1gyh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyh 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/1gyh_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=1gyh 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 D158A CELLVIBRIO CELLULOSA ALPHA-L-ARABINANASE MUTANT'''
+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>
-==Overview==
-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.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-GYH is a [[Single protein]] 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=1GYH OCA].
+</div>
+<div class="pdbe-citations 1gyh" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/12198486 12198486]
+*[[Arabinanase 3D structures|Arabinanase 3D structures]]
-[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Cellvibrio japonicus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Charnock, S J.]]
+[[Category: Charnock SJ]]
-[[Category: Davies, G J.]]
+[[Category: Davies GJ]]
-[[Category: Dodson, E J.]]
+[[Category: Dodson EJ]]
-[[Category: Gilbert, H J.]]
+[[Category: Gilbert HJ]]
-[[Category: Mckie, V A.]]
+[[Category: McKie VA]]
-[[Category: Nurizzo, D.]]
+[[Category: Nurizzo D]]
-[[Category: Roberts, S M.]]
+[[Category: Roberts SM]]
-[[Category: Taylor, E J.]]
+[[Category: Taylor EJ]]
-[[Category: Turkenburg, J P.]]
+[[Category: Turkenburg JP]]
-[[Category: Arabinanase]]
-[[Category: Catalysis]]
-[[Category: Cellvibrio]]
-[[Category: Hydrolase]]
-[[Category: Propeller]]
-[[Category: Pseudomona]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 18:10:50 2008''

1gyh

From Proteopedia

Current revision

Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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