6jqf

From Proteopedia

(Difference between revisions)

Current revision

Crystallization analysis of a beta-N-acetylhexosaminidase (Am2136) from Akkermansia muciniphila

Structural highlights

6jqf is a 1 chain structure with sequence from Akkermansia muciniphila ATCC BAA-835. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H2136_AKKM8 Potentially capable of cleaving the specific glycoside linkages in the process of mucin degradation in human intestinal tract (Probable). Hydrolyzes synthetic substrate pNP-beta-GlcNAc with high activity and pNP-beta-GalNAc to a lot lesser extent. Does not hydrolyze pNP-alpha-GalNAc.^[1]

Publication Abstract from PubMed

In this paper, we characterized Am2136 as a beta-N-acetylhexosaminidase from Akkermansia muciniphila to perform the biochemical characteristics and the crystal structure of selenomethionine-labeled Am2136 with GlcNAc complex. Crystallographic evidence suggests that an oxazolinium ion was formed intermediately by the 2-acetamido group during the substrate-assisted catalytic procedure. Structural and kinetic analysis of native Am2136 and D412A, E413A mutants were investigated and the results revealed substantial difference. The Kcat/Km value of D412A was decreased 4297-fold compared to native Am2136 revealed that mutation of Asp-412 results in preventing the 2-acetamido substituent from providing anchimeric assistance and thus reducing the catalytic efficiency. Moreover, Am2136 has a wide dependence on pH and temperature, while sensitive to divalent metal ions such as Ca(2+) and Mn(2+). These biochemical and crystallographic results provide evidences that Asp-412 residue assists to orient the 2-acetamido group for catalysis. Based on crystallographic evidence and sequence alignment with other GH family 20 enzymes, Asp-412 residue is possibly fundamental for Am2136 during substrate-assisted catalysis.

Biochemical characteristics and crystallographic evidence for substrate-assisted catalysis of a beta-N-acetylhexosaminidase in Akkermansia muciniphila.,Chen X, Li M, Wang Y, Tang R, Zhang M Biochem Biophys Res Commun. 2019 Sep 10;517(1):29-35. doi:, 10.1016/j.bbrc.2019.06.150. Epub 2019 Jul 23. PMID:31345574^[2]

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

References

↑ Chen X, Li M, Wang Y, Tang R, Zhang M. Biochemical characteristics and crystallographic evidence for substrate-assisted catalysis of a beta-N-acetylhexosaminidase in Akkermansia muciniphila. Biochem Biophys Res Commun. 2019 Sep 10;517(1):29-35. doi:, 10.1016/j.bbrc.2019.06.150. Epub 2019 Jul 23. PMID:31345574 doi:http://dx.doi.org/10.1016/j.bbrc.2019.06.150
↑ Chen X, Li M, Wang Y, Tang R, Zhang M. Biochemical characteristics and crystallographic evidence for substrate-assisted catalysis of a beta-N-acetylhexosaminidase in Akkermansia muciniphila. Biochem Biophys Res Commun. 2019 Sep 10;517(1):29-35. doi:, 10.1016/j.bbrc.2019.06.150. Epub 2019 Jul 23. PMID:31345574 doi:http://dx.doi.org/10.1016/j.bbrc.2019.06.150

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6jqf"

Categories: Akkermansia muciniphila ATCC BAA-835 | Large Structures | Chen X | Zhang M

@@ Line 3: / Line 3: @@
 <StructureSection load='6jqf' size='340' side='right'caption='[[6jqf]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6jqf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JQF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6jqf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Akkermansia_muciniphila_ATCC_BAA-835 Akkermansia muciniphila ATCC BAA-835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JQF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.9&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=6jqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqf OCA], [http://pdbe.org/6jqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jqf RCSB], [http://www.ebi.ac.uk/pdbsum/6jqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqf 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=6jqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqf OCA], [https://pdbe.org/6jqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jqf RCSB], [https://www.ebi.ac.uk/pdbsum/6jqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqf ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/H2136_AKKM8 H2136_AKKM8] Potentially capable of cleaving the specific glycoside linkages in the process of mucin degradation in human intestinal tract (Probable). Hydrolyzes synthetic substrate pNP-beta-GlcNAc with high activity and pNP-beta-GalNAc to a lot lesser extent. Does not hydrolyze pNP-alpha-GalNAc.<ref>PMID:31345574</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 19: @@
 </div>
 <div class="pdbe-citations 6jqf" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Beta-N-acetylhexosaminidase 3D structures|Beta-N-acetylhexosaminidase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Akkermansia muciniphila ATCC BAA-835]]
 [[Category: Large Structures]]
-[[Category: Chen, X]]
+[[Category: Chen X]]
-[[Category: Zhang, M]]
+[[Category: Zhang M]]
-[[Category: Akkermansia muciniphila]]
-[[Category: Catalytic mechanism]]
-[[Category: Crystallographic evidence]]
-[[Category: Hydrolase]]
-[[Category: Keywords:beta-n-acetylhexosaminida]]

6jqf

From Proteopedia

Current revision

Crystallization analysis of a beta-N-acetylhexosaminidase (Am2136) from Akkermansia muciniphila

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox