1hp4: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:1hp4.png|left|200px]]


<!--
==CRYSTAL STRUCTURE OF STREPTOMYCES PLICATUS BETA-N-ACETYLHEXOSAMINIDASE==
The line below this paragraph, containing "STRUCTURE_1hp4", creates the "Structure Box" on the page.
<StructureSection load='1hp4' size='340' side='right'caption='[[1hp4]], [[Resolution|resolution]] 2.20&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'>[[1hp4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_plicatus Streptomyces plicatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HP4 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]] 2.2&#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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_1hp4|  PDB=1hp4  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1hp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hp4 OCA], [https://pdbe.org/1hp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hp4 RCSB], [https://www.ebi.ac.uk/pdbsum/1hp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hp4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O85361_STRPL O85361_STRPL]
== 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/hp/1hp4_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=1hp4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
beta-Hexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of beta-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. Heritable deficiency of this enzyme results in various forms of GalNAc-beta(1,4)-[N-acetylneuraminic acid (2,3)]-Gal-beta(1,4)-Glc-ceramide gangliosidosis, including Tay-Sachs disease. We have determined the x-ray crystal structure of a beta-hexosaminidase from Streptomyces plicatus to 2.2 A resolution (Protein Data Bank code ). beta-Hexosaminidases are believed to use a substrate-assisted catalytic mechanism that generates a cyclic oxazolinium ion intermediate. We have solved and refined a complex between the cyclic intermediate analogue N-acetylglucosamine-thiazoline and beta-hexosaminidase from S. plicatus to 2.1 A resolution (Protein Data Bank code ). Difference Fourier analysis revealed the pyranose ring of N-acetylglucosamine-thiazoline bound in the enzyme active site with a conformation close to that of a (4)C(1) chair. A tryptophan-lined hydrophobic pocket envelopes the thiazoline ring, protecting it from solvolysis at the iminium ion carbon. Within this pocket, Tyr(393) and Asp(313) appear important for positioning the 2-acetamido group of the substrate for nucleophilic attack at the anomeric center and for dispersing the positive charge distributed into the oxazolinium ring upon cyclization. This complex provides decisive structural evidence for substrate-assisted catalysis and the formation of a covalent, cyclic intermediate in family 20 beta-hexosaminidases.


===CRYSTAL STRUCTURE OF STREPTOMYCES PLICATUS BETA-N-ACETYLHEXOSAMINIDASE===
Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase.,Mark BL, Vocadlo DJ, Knapp S, Triggs-Raine BL, Withers SG, James MN J Biol Chem. 2001 Mar 30;276(13):10330-7. Epub 2000 Dec 21. PMID:11124970<ref>PMID:11124970</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1hp4" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_11124970}}, adds the Publication Abstract to the page
*[[Beta-Hexosaminidase|Beta-Hexosaminidase]]
(as it appears on PubMed at http://www.pubmed.gov), where 11124970 is the PubMed ID number.
*[[Beta-Hexosaminidase 3D structures|Beta-Hexosaminidase 3D structures]]
-->
*[[Beta-N-acetylhexosaminidase 3D structures|Beta-N-acetylhexosaminidase 3D structures]]
{{ABSTRACT_PUBMED_11124970}}
== References ==
 
<references/>
==About this Structure==
__TOC__
1HP4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_plicatus Streptomyces plicatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HP4 OCA].
</StructureSection>
 
[[Category: Large Structures]]
==Reference==
Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase., Mark BL, Vocadlo DJ, Knapp S, Triggs-Raine BL, Withers SG, James MN, J Biol Chem. 2001 Mar 30;276(13):10330-7. Epub 2000 Dec 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11124970 11124970]
[[Category: Beta-N-acetylhexosaminidase]]
[[Category: Single protein]]
[[Category: Streptomyces plicatus]]
[[Category: Mark, B L.]]
[[Category: Family 20]]
[[Category: Glycosyl hydrolase]]
[[Category: Hexosaminidase]]
[[Category: Streptomyces plicatus]]
[[Category: Streptomyces plicatus]]
[[Category: Tim barrel]]
[[Category: Mark BL]]
[[Category: X-ray]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 08:29:28 2008''
Retrieved from "https://proteopedia.org/1hp4"