5oar: Difference between revisions

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<StructureSection load='5oar' size='340' side='right'caption='[[5oar]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='5oar' size='340' side='right'caption='[[5oar]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5oar]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OAR FirstGlance]. <br>
<table><tr><td colspan='2'>[[5oar]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OAR FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NGT:3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL'>NGT</scene>, <scene name='pdbligand=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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]] 2.3&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NGT:3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL'>NGT</scene>, <scene name='pdbligand=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5oar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oar OCA], [http://pdbe.org/5oar PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oar RCSB], [http://www.ebi.ac.uk/pdbsum/5oar PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oar ProSAT]</span></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=5oar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oar OCA], [https://pdbe.org/5oar PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oar RCSB], [https://www.ebi.ac.uk/pdbsum/5oar PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oar ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HEXA_ASPOZ HEXA_ASPOZ] Selectively hydrolyzes GlcNAcbeta(1->4)GlcNAc (N,N'-diacetylchitobiose) and Gal-NAcbeta(1->4)GlcNAc, but not their C-2 epimers GlcNAcbeta(1->4)ManNAc or Gal-NAcbeta(1->4)ManNAc. However, hydrolyzes both GlcNAcbeta(1->6)GlcNAc and GlcNAcbeta(1->6)ManNAc (Ref.7). Part of the binary chitinolytic system. Involved in hydrolyzation of chitobiose and higher chito-oligomers (produced from cell wall chitin by endochitinases), thus contributing to the formation of germ tubes, fruit-bodies and septa during hyphenation (Probable). Hydrolyzes synthetic substrate p-nitrophenyl-beta-N-acetyl-D-glucosaminide (pNP-GlcNAc) (PubMed:17302431, PubMed:12723619, Ref.7). Hydrolyzes synthetic substrate p-nitrophenyl-beta-N-acetyl-D-galactosaminide (pNP-GalNAc) (PubMed:12723619). Hydrolyzes chromogenic substrate 4-nitrophenyl-2-acetamido-2-deoxyglucopyranoside (PubMed:21505251, PubMed:17509134, PubMed:29239122).<ref>PMID:12723619</ref> <ref>PMID:17302431</ref> <ref>PMID:17509134</ref> <ref>PMID:21505251</ref> <ref>PMID:29239122</ref> <ref>PMID:15494009</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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*[[Beta-Hexosaminidase|Beta-Hexosaminidase]]
*[[Beta-Hexosaminidase|Beta-Hexosaminidase]]
*[[Beta-Hexosaminidase 3D structures|Beta-Hexosaminidase 3D structures]]
*[[Beta-Hexosaminidase 3D structures|Beta-Hexosaminidase 3D structures]]
*[[Beta-N-acetylhexosaminidase 3D structures|Beta-N-acetylhexosaminidase 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Aspergillus oryzae]]
[[Category: Aspergillus oryzae]]
[[Category: Beta-N-acetylhexosaminidase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Brynda, J]]
[[Category: Brynda J]]
[[Category: Otwinowski, Z]]
[[Category: Otwinowski Z]]
[[Category: Pachl, P]]
[[Category: Pachl P]]
[[Category: Rezacova, P]]
[[Category: Rezacova P]]
[[Category: Skerlova, J]]
[[Category: Skerlova J]]
[[Category: Vanek, O]]
[[Category: Vanek O]]
[[Category: Carbohydrate biotechnology]]
[[Category: Glycosylation]]
[[Category: Hydrolase]]
[[Category: Propeptide]]

Revision as of 12:38, 6 December 2023

Crystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzaeCrystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae

Structural highlights

5oar is a 4 chain structure with sequence from Aspergillus oryzae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HEXA_ASPOZ Selectively hydrolyzes GlcNAcbeta(1->4)GlcNAc (N,N'-diacetylchitobiose) and Gal-NAcbeta(1->4)GlcNAc, but not their C-2 epimers GlcNAcbeta(1->4)ManNAc or Gal-NAcbeta(1->4)ManNAc. However, hydrolyzes both GlcNAcbeta(1->6)GlcNAc and GlcNAcbeta(1->6)ManNAc (Ref.7). Part of the binary chitinolytic system. Involved in hydrolyzation of chitobiose and higher chito-oligomers (produced from cell wall chitin by endochitinases), thus contributing to the formation of germ tubes, fruit-bodies and septa during hyphenation (Probable). Hydrolyzes synthetic substrate p-nitrophenyl-beta-N-acetyl-D-glucosaminide (pNP-GlcNAc) (PubMed:17302431, PubMed:12723619, Ref.7). Hydrolyzes synthetic substrate p-nitrophenyl-beta-N-acetyl-D-galactosaminide (pNP-GalNAc) (PubMed:12723619). Hydrolyzes chromogenic substrate 4-nitrophenyl-2-acetamido-2-deoxyglucopyranoside (PubMed:21505251, PubMed:17509134, PubMed:29239122).[1] [2] [3] [4] [5] [6]

Publication Abstract from PubMed

beta-N-acetylhexosaminidase from the fungus Aspergillus oryzae is a secreted extracellular enzyme that cleaves chitobiose into constituent monosaccharides. It belongs to the GH 20 glycoside hydrolase family and consists of two N-glycosylated catalytic cores noncovalently associated with two 10-kDa O-glycosylated propeptides. We used X-ray diffraction and mass spectrometry to determine the structure of Aspergillus oryzae beta-N-acetylhexosaminidase isolated from its natural source. The three-dimensional structure determined and refined to a resolution of 2.3 A revealed that this enzyme is active as a uniquely tight dimeric assembly further stabilized by N- and O-glycosylation. The propeptide from one subunit forms extensive noncovalent interactions with the catalytic core of the second subunit in the dimer, and this chain swap suggests the distinctive structural mechanism of the enzyme's activation. Unique structural features of beta-N-acetylhexosaminidase from Aspergillus oryzae define a very stable and robust framework suitable for biotechnological applications. The crystal structure reported here provides structural insights into the enzyme architecture as well as the detailed configuration of the active site. These insights can be applied to rational enzyme engineering. This article is protected by copyright. All rights reserved.

Crystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae sheds light onto its substrate specificity, high stability, and regulation by propeptide.,Skerlova J, Blaha J, Pachl P, Hofbauerova K, Kukacka Z, Man P, Pompach P, Novak P, Otwinowski Z, Brynda J, Vanek O, Rezacova P FEBS J. 2017 Dec 14. doi: 10.1111/febs.14360. PMID:29239122[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Matsuo I, Kim S, Yamamoto Y, Ajisaka K, Maruyama JI, Nakajima H, Kitamoto K. Cloning and overexpression of beta-N-acetylglucosaminidase encoding gene nagA from Aspergillus oryzae and enzyme-catalyzed synthesis of human milk oligosaccharide. Biosci Biotechnol Biochem. 2003 Mar;67(3):646-50. PMID:12723619 doi:10.1271/bbb.67.646
  2. ↑ Plíhal O, Sklenár J, Hofbauerová K, Novák P, Man P, Pompach P, Kavan D, Ryslavá H, Weignerová L, Charvátová-Pisvejcová A, Kren V, Bezouska K. Large propeptides of fungal beta-N-acetylhexosaminidases are novel enzyme regulators that must be intracellularly processed to control activity, dimerization, and secretion into the extracellular environment. Biochemistry. 2007 Mar 13;46(10):2719-34. PMID:17302431 doi:10.1021/bi061828m
  3. ↑ Ettrich R, Kopecký V Jr, Hofbauerová K, Baumruk V, Novák P, Pompach P, Man P, Plíhal O, Kutý M, Kulik N, Sklenár J, Ryslavá H, Kren V, Bezouska K. Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies. BMC Struct Biol. 2007 May 17;7:32. PMID:17509134 doi:10.1186/1472-6807-7-32
  4. ↑ Vaněk O, Brynda J, Hofbauerová K, Kukačka Z, Pachl P, Bezouška K, Rezáčová P. Crystallization and diffraction analysis of β-N-acetylhexosaminidase from Aspergillus oryzae. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Apr 1;67(Pt 4):498-503. PMID:21505251 doi:10.1107/S1744309111004945
  5. ↑ Skerlova J, Blaha J, Pachl P, Hofbauerova K, Kukacka Z, Man P, Pompach P, Novak P, Otwinowski Z, Brynda J, Vanek O, Rezacova P. Crystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae sheds light onto its substrate specificity, high stability, and regulation by propeptide. FEBS J. 2017 Dec 14. doi: 10.1111/febs.14360. PMID:29239122 doi:http://dx.doi.org/10.1111/febs.14360
  6. ↑ Plíhal O, Sklenár J, Kmonícková J, Man P, Pompach P, Havlícek V, Kren V, Bezouska K. N-glycosylated catalytic unit meets O-glycosylated propeptide: complex protein architecture in a fungal hexosaminidase. Biochem Soc Trans. 2004 Nov;32(Pt 5):764-5. PMID:15494009 doi:10.1042/BST0320764
  7. ↑ Skerlova J, Blaha J, Pachl P, Hofbauerova K, Kukacka Z, Man P, Pompach P, Novak P, Otwinowski Z, Brynda J, Vanek O, Rezacova P. Crystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae sheds light onto its substrate specificity, high stability, and regulation by propeptide. FEBS J. 2017 Dec 14. doi: 10.1111/febs.14360. PMID:29239122 doi:http://dx.doi.org/10.1111/febs.14360

5oar, resolution 2.30Å

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