8p0l

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide

Structural highlights

8p0l is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OGA_HUMAN Isoform 1: Cleaves GlcNAc but not GalNAc from O-glycosylated proteins. Can use p-nitrophenyl-beta-GlcNAc and 4-methylumbelliferone-GlcNAc as substrates but not p-nitrophenyl-beta-GalNAc or p-nitrophenyl-alpha-GlcNAc (in vitro) (PubMed:11148210). Does not bind acetyl-CoA and does not have histone acetyltransferase activity (PubMed:24088714).^[1] ^[2] ^[3] ^[4] ^[5] Isoform 3: Cleaves GlcNAc but not GalNAc from O-glycosylated proteins. Can use p-nitrophenyl-beta-GlcNAc as substrate but not p-nitrophenyl-beta-GalNAc or p-nitrophenyl-alpha-GlcNAc (in vitro), but has about six times lower specific activity than isoform 1.^[6]

Publication Abstract from PubMed

Human O-linked beta-N-acetylglucosaminidase (hOGA) is one of the two enzymes involved in nuclear and cytoplasmic protein O-GlcNAcylation, an essential post-translational modification. The enzyme catalyzes the hydrolysis of the GlcNAc-O-(Ser/Thr) glycosidic bonds via anchimeric assistance through the 2-acetamido group of the GlcNAc sugar. However, the conformational itinerary of the GlcNAc ring during catalysis remains unclear. Here we report the crystal structure of wild type hOGA in complex with a nonhydrolyzable glycopeptide substrate and elucidate the full enzyme catalytic mechanism using QM/MM metadynamics. We show that the enzyme can bind the substrate in either a chair- or a boat-like conformation, but only the latter is catalytically competent, leading to the reaction products via (1,4)B/(1)S(3) --> [(4)E](double dagger) --> (4)C(1) and (4)C(1) --> [(4)E](double dagger) --> (1,4)B/(1)S(3) conformational itineraries for the first and second catalytic reaction steps, respectively. Our results reconcile previous experimental observations for human and bacterial OGA and will aid the development of more effective OGA inhibitors for diseases associated with impaired O-GlcNAcylation.

Human O-GlcNAcase Uses a Preactivated Boat-skew Substrate Conformation for Catalysis. Evidence from X-ray Crystallography and QM/MM Metadynamics.,Calvelo M, Males A, Alteen MG, Willems LI, Vocadlo DJ, Davies GJ, Rovira C ACS Catal. 2023 Oct 10;13(20):13672-13678. doi: 10.1021/acscatal.3c02378. , eCollection 2023 Oct 20. PMID:37969138^[7]

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

References

↑ Gao Y, Wells L, Comer FI, Parker GJ, Hart GW. Dynamic O-glycosylation of nuclear and cytosolic proteins: cloning and characterization of a neutral, cytosolic beta-N-acetylglucosaminidase from human brain. J Biol Chem. 2001 Mar 30;276(13):9838-45. Epub 2001 Jan 8. PMID:11148210 doi:http://dx.doi.org/10.1074/jbc.M010420200
↑ Wells L, Gao Y, Mahoney JA, Vosseller K, Chen C, Rosen A, Hart GW. Dynamic O-glycosylation of nuclear and cytosolic proteins: further characterization of the nucleocytoplasmic beta-N-acetylglucosaminidase, O-GlcNAcase. J Biol Chem. 2002 Jan 18;277(3):1755-61. PMID:11788610
↑ Li J, Huang CL, Zhang LW, Lin L, Li ZH, Zhang FW, Wang P. Isoforms of human O-GlcNAcase show distinct catalytic efficiencies. Biochemistry (Mosc). 2010 Jul;75(7):938-43. PMID:20673219
↑ Schimpl M, Borodkin VS, Gray LJ, van Aalten DM. Synergy of Peptide and Sugar in O-GlcNAcase Substrate Recognition. Chem Biol. 2012 Feb 24;19(2):173-8. PMID:22365600 doi:10.1016/j.chembiol.2012.01.011
↑ Rao FV, Schuttelkopf AW, Dorfmueller HC, Ferenbach AT, Navratilova I, van Aalten DM. Structure of a bacterial putative acetyltransferase defines the fold of the human O-GlcNAcase C-terminal domain. Open Biol. 2013 Oct 2;3(10):130021. PMID:24088714 doi:http://dx.doi.org/10.1098/rsob.130021
↑ Li J, Huang CL, Zhang LW, Lin L, Li ZH, Zhang FW, Wang P. Isoforms of human O-GlcNAcase show distinct catalytic efficiencies. Biochemistry (Mosc). 2010 Jul;75(7):938-43. PMID:20673219
↑ Calvelo M, Males A, Alteen MG, Willems LI, Vocadlo DJ, Davies GJ, Rovira C. Human O-GlcNAcase Uses a Preactivated Boat-skew Substrate Conformation for Catalysis. Evidence from X-ray Crystallography and QM/MM Metadynamics. ACS Catal. 2023 Oct 10;13(20):13672-13678. PMID:37969138 doi:10.1021/acscatal.3c02378

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8p0l"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8p0l is ON HOLD  until Paper Publication
+==Crystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide==
+<StructureSection load='8p0l' size='340' side='right'caption='[[8p0l]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8p0l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8P0L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8P0L FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene></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=8p0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8p0l OCA], [https://pdbe.org/8p0l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8p0l RCSB], [https://www.ebi.ac.uk/pdbsum/8p0l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8p0l ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OGA_HUMAN OGA_HUMAN] Isoform 1: Cleaves GlcNAc but not GalNAc from O-glycosylated proteins. Can use p-nitrophenyl-beta-GlcNAc and 4-methylumbelliferone-GlcNAc as substrates but not p-nitrophenyl-beta-GalNAc or p-nitrophenyl-alpha-GlcNAc (in vitro) (PubMed:11148210). Does not bind acetyl-CoA and does not have histone acetyltransferase activity (PubMed:24088714).<ref>PMID:11148210</ref> <ref>PMID:11788610</ref> <ref>PMID:20673219</ref> <ref>PMID:22365600</ref> <ref>PMID:24088714</ref>   Isoform 3: Cleaves GlcNAc but not GalNAc from O-glycosylated proteins. Can use p-nitrophenyl-beta-GlcNAc as substrate but not p-nitrophenyl-beta-GalNAc or p-nitrophenyl-alpha-GlcNAc (in vitro), but has about six times lower specific activity than isoform 1.<ref>PMID:20673219</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human O-linked beta-N-acetylglucosaminidase (hOGA) is one of the two enzymes involved in nuclear and cytoplasmic protein O-GlcNAcylation, an essential post-translational modification. The enzyme catalyzes the hydrolysis of the GlcNAc-O-(Ser/Thr) glycosidic bonds via anchimeric assistance through the 2-acetamido group of the GlcNAc sugar. However, the conformational itinerary of the GlcNAc ring during catalysis remains unclear. Here we report the crystal structure of wild type hOGA in complex with a nonhydrolyzable glycopeptide substrate and elucidate the full enzyme catalytic mechanism using QM/MM metadynamics. We show that the enzyme can bind the substrate in either a chair- or a boat-like conformation, but only the latter is catalytically competent, leading to the reaction products via (1,4)B/(1)S(3) --&gt; [(4)E](double dagger) --&gt; (4)C(1) and (4)C(1) --&gt; [(4)E](double dagger) --&gt; (1,4)B/(1)S(3) conformational itineraries for the first and second catalytic reaction steps, respectively. Our results reconcile previous experimental observations for human and bacterial OGA and will aid the development of more effective OGA inhibitors for diseases associated with impaired O-GlcNAcylation.
-Authors: Males, A., Davies, G.J., Calvelo, M., Alteen, M.G., Vocadlo, D.J., Rovira, C.
+Human O-GlcNAcase Uses a Preactivated Boat-skew Substrate Conformation for Catalysis. Evidence from X-ray Crystallography and QM/MM Metadynamics.,Calvelo M, Males A, Alteen MG, Willems LI, Vocadlo DJ, Davies GJ, Rovira C ACS Catal. 2023 Oct 10;13(20):13672-13678. doi: 10.1021/acscatal.3c02378. , eCollection 2023 Oct 20. PMID:37969138<ref>PMID:37969138</ref>
-Description: Crystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Davies, G.J]]
+<div class="pdbe-citations 8p0l" style="background-color:#fffaf0;"></div>
-[[Category: Rovira, C]]
+== References ==
-[[Category: Alteen, M.G]]
+<references/>
-[[Category: Males, A]]
+__TOC__
-[[Category: Vocadlo, D.J]]
+</StructureSection>
-[[Category: Calvelo, M]]
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Alteen MG]]
+[[Category: Calvelo M]]
+[[Category: Davies GJ]]
+[[Category: Males A]]
+[[Category: Rovira C]]
+[[Category: Vocadlo DJ]]

8p0l

From Proteopedia

Current revision

Crystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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