9mqc

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m (Protected "9mqc" [edit=sysop:move=sysop])
Current revision (07:28, 8 October 2025) (edit) (undo)
 
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'''Unreleased structure'''
 
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The entry 9mqc is ON HOLD
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==Vitamin K-dependent gamma-carboxylase with Osteocalcin (mutant) and vitamin K hydroquinone==
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<StructureSection load='9mqc' size='340' side='right'caption='[[9mqc]], [[Resolution|resolution]] 3.13&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[9mqc]] 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=9MQC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9MQC FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.13&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PL:(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM+4-OXIDE'>6PL</scene>, <scene name='pdbligand=A1AVC:2-methyl-3-[(~{E},7~{R},11~{R})-3,7,11,15-tetramethylhexadec-2-enyl]naphthalene-1,4-diol'>A1AVC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9mqc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9mqc OCA], [https://pdbe.org/9mqc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9mqc RCSB], [https://www.ebi.ac.uk/pdbsum/9mqc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9mqc ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/VKGC_HUMAN VKGC_HUMAN] Pseudoxanthoma elasticum-like skin manifestations with retinitis pigmentosa;Hereditary combined deficiency of vitamin K-dependent clotting factors;Body skin hyperlaxity due to vitamin K-dependent coagulation factor deficiency. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry.
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== Function ==
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[https://www.uniprot.org/uniprot/VKGC_HUMAN VKGC_HUMAN] Mediates the vitamin K-dependent carboxylation of glutamate residues to calcium-binding gamma-carboxyglutamate (Gla) residues with the concomitant conversion of the reduced hydroquinone form of vitamin K to vitamin K epoxide (PubMed:17073445). Catalyzes gamma-carboxylation of various proteins, such as blood coagulation factors (F2, F7, F9 and F10), osteocalcin (BGLAP) or matrix Gla protein (MGP) (PubMed:17073445).<ref>PMID:17073445</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The gamma-carboxylation state of osteocalcin determines its essential functions in bone mineralization or systemic metabolism and serves as a prominent biomarker for bone health and vitamin K nutrition. This post-translational modification of glutamate residues is catalyzed by the membrane-embedded vitamin K-dependent gamma-carboxylase (VKGC), which typically recognizes protein substrates through their tightly bound propeptide that triggers gamma-carboxylation. However, the osteocalcin propeptide exhibits negligible affinity for VKGC. To understand the underlying molecular mechanism, we determined the cryo-electron microscopy structures of VKGC with osteocalcin carrying a native propeptide or a high-affinity variant at different carboxylation states. The structures reveal a large chamber in VKGC that maintains uncarboxylated and partially carboxylated osteocalcin in partially unfolded conformations, allowing their glutamate-rich region and C-terminal helices to engage with VKGC at multiple sites. Binding of this mature region together with the low-affinity propeptide effectively stimulates VKGC activity, similar to high-affinity propeptides that differ only in closely fitting interactions. However, the low-affinity propeptide renders osteocalcin prone to undercarboxylation at low vitamin K levels, thereby serving as a discernible biomarker. Overall, our studies reveal the unique interaction of osteocalcin with VKGC and provide a framework for designing therapeutic strategies targeting osteocalcin-related bone and metabolic disorders.
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Authors: Li, W., Liu, B., Cao, Q.
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Structural insights into the vitamin K-dependent gamma-carboxylation of osteocalcin.,Cao Q, Fan J, Ammerman A, Awasthi S, Lin Z, Mierxiati S, Chen H, Xu J, Garcia BA, Liu B, Li W Cell Res. 2025 Oct;35(10):735-749. doi: 10.1038/s41422-025-01161-0. Epub 2025 Sep , 2. PMID:40890294<ref>PMID:40890294</ref>
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Description: Vitamin K-dependent gamma-carboxylase with Osteocalcin (mutant) and vitamin K hydroquinone
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Li, W]]
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<div class="pdbe-citations 9mqc" style="background-color:#fffaf0;"></div>
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[[Category: Liu, B]]
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== References ==
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[[Category: Cao, Q]]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Cao Q]]
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[[Category: Li W]]
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[[Category: Liu B]]

Current revision

Vitamin K-dependent gamma-carboxylase with Osteocalcin (mutant) and vitamin K hydroquinone

PDB ID 9mqc

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