1nof: Difference between revisions

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[[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''

Latest revision as of 10:58, 14 February 2024

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

Structural highlights

1nof is a 1 chain structure with sequence from Dickeya chrysanthemi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.42Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q46961_DICCH

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1nof, resolution 1.42Å

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