This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1nof

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:58, 14 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1nof.gif|left|200px]]
 
-
{{Structure
+
==THE FIRST CRYSTALLOGRAPHIC STRUCTURE OF A XYLANASE FROM GLYCOSYL HYDROLASE FAMILY 5: IMPLICATIONS FOR CATALYSIS==
-
|PDB= 1nof |SIZE=350|CAPTION= <scene name='initialview01'>1nof</scene>, resolution 1.42&Aring;
+
<StructureSection load='1nof' size='340' side='right'caption='[[1nof]], [[Resolution|resolution]] 1.42&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=ACI:Catalytic+Acid/Base'>ACI</scene> and <scene name='pdbsite=NUC:Catalytic+Nucleophile'>NUC</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>
+
<table><tr><td colspan='2'>[[1nof]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dickeya_chrysanthemi Dickeya chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NOF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NOF FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.42&#8491;</td></tr>
-
|GENE= xynA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=556 Erwinia chrysanthemi])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nof OCA], [https://pdbe.org/1nof PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nof RCSB], [https://www.ebi.ac.uk/pdbsum/1nof PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nof ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nof OCA], [http://www.ebi.ac.uk/pdbsum/1nof PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nof RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/Q46961_DICCH Q46961_DICCH]
-
 
+
== Evolutionary Conservation ==
-
'''THE FIRST CRYSTALLOGRAPHIC STRUCTURE OF A XYLANASE FROM GLYCOSYL HYDROLASE FAMILY 5: IMPLICATIONS FOR CATALYSIS'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/no/1nof_consurf.spt"</scriptWhenChecked>
-
The room-temperature structure of xylanase (EC 3.2.1.8) from the bacterial plant pathogen Erwinia chrysanthemi expressed in Escherichia coli, a 45 kDa, 413-amino acid protein belonging to glycoside hydrolase family 5, has been determined by multiple isomorphous replacement and refined to a resolution of 1.42 A. This represents the first structure of a xylanase not belonging to either glycoside hydrolase family 10 or family 11. The enzyme is composed of two domains similar to most family 10 xylanases and the alpha-amylases. The catalytic domain (residues 46-315) has a (beta/alpha)(8)-barrel motif with a binding cleft along the C-terminal side of the beta-barrel. The catalytic residues, Glu165 and Glu253, determined by correspondence to other family 5 and family 10 glycoside hydrolases, lie inside this cleft on the C-terminal ends of beta-strands 4 and 7, respectively, with an O(epsilon)2...O(epsilon)1 distance of 4.22 A. The smaller domain (residues 31-43 and 323-413) has a beta(9)-barrel motif with five of the strands interfacing with alpha-helices 7 and 8 of the catalytic domain. The first 13 N-terminal residues form one beta-strand of this domain. Residues 44, 45, and 316-322 form the linkers between this domain and the catalytic domain.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1NOF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Erwinia_chrysanthemi Erwinia chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NOF OCA].
+
</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=1nof ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
__TOC__
-
First crystallographic structure of a xylanase from glycoside hydrolase family 5: implications for catalysis., Larson SB, Day J, Barba de la Rosa AP, Keen NT, McPherson A, Biochemistry. 2003 Jul 22;42(28):8411-22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12859186 12859186]
+
</StructureSection>
-
[[Category: Endo-1,4-beta-xylanase]]
+
[[Category: Dickeya chrysanthemi]]
-
[[Category: Erwinia chrysanthemi]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Barba De La Rosa AP]]
-
[[Category: Day, J.]]
+
[[Category: Day J]]
-
[[Category: Keen, N T.]]
+
[[Category: Keen NT]]
-
[[Category: Larson, S B.]]
+
[[Category: Larson SB]]
-
[[Category: McPherson, A.]]
+
[[Category: McPherson A]]
-
[[Category: Rosa, A P.Barba De La.]]
+
-
[[Category: carbohydrate-binding module]]
+
-
[[Category: catalytic domain]]
+
-
[[Category: glycohydrolase family 5]]
+
-
[[Category: xylanase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:33:11 2008''
+

Current revision

THE FIRST CRYSTALLOGRAPHIC STRUCTURE OF A XYLANASE FROM GLYCOSYL HYDROLASE FAMILY 5: IMPLICATIONS FOR CATALYSIS

PDB ID 1nof

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nof"
Personal tools