3alf: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Class V Chitinase from Nicotiana tobaccum==
-<StructureSection load='3alf' size='340' side='right' caption='[[3alf]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
+<StructureSection load='3alf' size='340' side='right'caption='[[3alf]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3alf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/American_tobacco American tobacco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ALF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ALF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3alf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nicotiana_tabacum Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ALF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ALF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3alg|3alg]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">chi-V ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4097 American tobacco])</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=3alf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3alf OCA], [https://pdbe.org/3alf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3alf RCSB], [https://www.ebi.ac.uk/pdbsum/3alf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3alf ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chitinase Chitinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.14 3.2.1.14] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3alf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3alf OCA], [http://pdbe.org/3alf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3alf RCSB], [http://www.ebi.ac.uk/pdbsum/3alf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3alf ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/Q43576_TOBAC Q43576_TOBAC]
-A class V chitinase from Nicotiana tabacum (NtChiV) with amino acid sequence similar to that of Serratia marcescens chitinase B (SmChiB) was expressed in E. coli and purified to homogeneity. When N-acetylglucosamine oligosaccharides [(NAG)(n)] were hydrolyzed by the purified NtChiV, the second glycosidic linkage from the non-reducing end was predominantly hydrolyzed in a manner similar to that of SmChiB. NtChiV was shown to hydrolyze partially N-acetylated chitosan non-processively, whereas SmChiB hydrolyzes the same substrate processively. The crystal structure of NtChiV was determined by the single-wavelength anomalous dispersion method at 1.2 A resolution. The protein adopts a classical (beta/alpha)-barrel fold (residues 1-233 and 303-348) with an insertion of a small (alpha + beta) domain (residues 234-302). This is the first crystal structure of a plant class V chitinase. The crystal structure of the inactive mutant NtChiV E115Q complexed with (NAG) was also solved and exhibited a linear conformation of the bound oligosaccharide occupying -2, +1, +2, and +3 subsites. The complex structure corresponds to an initial state of (NAG) binding, which is proposed to be converted into a bent conformation through sliding of the +1, +2, and +3 sugar units to -1, +1, and +2 subsites. Although NtChiV is similar to SmChiB, the chitin-binding domain is present in the C-terminus of the latter, but not in the former. Aromatic amino acid residues found in the substrate binding cleft of SmChiB, including Trp97, are substituted with aliphatic residues in NtChiV. These structural differences appear to be responsible for NtChiV being a non-processive enzyme.
-Crystal structure and mode of action of a class V chitinase from Nicotiana tabacum.,Ohnuma T, Numata T, Osawa T, Mizuhara M, Varum KM, Fukamizo T Plant Mol Biol. 2011 Feb;75(3):291-304. Epub 2011 Jan 15. PMID:21240541<ref>PMID:21240541</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3alf" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Chitinase|Chitinase]]
+*[[Chitinase 3D structures|Chitinase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: American tobacco]]
+[[Category: Large Structures]]
-[[Category: Chitinase]]
+[[Category: Nicotiana tabacum]]
-[[Category: Fukamizo, T]]
+[[Category: Fukamizo T]]
-[[Category: Numata, T]]
+[[Category: Numata T]]
-[[Category: Ohnuma, T]]
+[[Category: Ohnuma T]]
-[[Category: Osawa, T]]
+[[Category: Osawa T]]
-[[Category: Hydrolase]]