5epp: Difference between revisions

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-'''Unreleased structure'''
-The entry 5epp is ON HOLD  until Paper Publication
+==Crystal structure of P97 N-terminal domain in complex with a helix==
+<StructureSection load='5epp' size='340' side='right' caption='[[5epp]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5epp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EPP FirstGlance]. <br>
+</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Vesicle-fusing_ATPase Vesicle-fusing ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.6 3.6.4.6] </span></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=5epp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5epp OCA], [http://pdbe.org/5epp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5epp RCSB], [http://www.ebi.ac.uk/pdbsum/5epp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5epp ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[[http://www.uniprot.org/uniprot/TERA_HUMAN TERA_HUMAN]] Defects in VCP are the cause of inclusion body myopathy with early-onset Paget disease and frontotemporal dementia (IBMPFD) [MIM:[http://omim.org/entry/167320 167320]]; also known as muscular dystrophy, limb-girdle, with Paget disease of bone or pagetoid amyotrophic lateral sclerosis or pagetoid neuroskeletal syndrome or lower motor neuron degeneration with Paget-like bone disease. IBMPFD features adult-onset proximal and distal muscle weakness (clinically resembling limb girdle muscular dystrophy), early-onset Paget disease of bone in most cases and premature frontotemporal dementia.<ref>PMID:20512113</ref> <ref>PMID:15034582</ref> <ref>PMID:15732117</ref> <ref>PMID:16247064</ref> <ref>PMID:16321991</ref>   Defects in VCP are the cause of amyotrophic lateral sclerosis type 14 with or without frontotemporal dementia (ALS14) [MIM:[http://omim.org/entry/613954 613954]]. ALS14 is a neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5-10% of the cases. Patients with ALS14 may develop frontotemporal dementia.<ref>PMID:21145000</ref>
+== Function ==
+[[http://www.uniprot.org/uniprot/TERA_HUMAN TERA_HUMAN]] Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR. Also involved in DNA damage response: recruited to double-strand breaks (DSBs) sites in a RNF8- and RNF168-dependent manner and promotes the recruitment of TP53BP1 at DNA damage sites. Recruited to stalled replication forks by SPRTN: may act by mediating extraction of DNA polymerase eta (POLH) to prevent excessive translesion DNA synthesis and limit the incidence of mutations induced by DNA damage.<ref>PMID:15456787</ref> <ref>PMID:16168377</ref> <ref>PMID:22020440</ref> <ref>PMID:22120668</ref> <ref>PMID:22607976</ref> <ref>PMID:23042607</ref> <ref>PMID:23042605</ref>  [[http://www.uniprot.org/uniprot/RHBL4_HUMAN RHBL4_HUMAN]] Intramembrane-cleaving serine protease that cleaves single transmembrane or multi-pass membrane proteins in the hydrophobic plane of the membrane, luminal loops and juxtamembrane regions. Involved in regulated intramembrane proteolysis and the subsequent release of functional polypeptides from their membrane anchors. Functional component of endoplasmic reticulum-associated degradation (ERAD) for misfolded membrane proteins. Required for the degradation process of some specific misfolded endoplasmic reticulum (ER) luminal proteins. Participates in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner. Functions in BIK, MPZ, PKD1, PTCRA, RHO, STEAP3 and TRAC processing. Involved in the regulation of exosomal secretion; inhibits the TSAP6-mediated secretion pathway. Involved in the regulation of apoptosis; modulates BIK-mediated apoptotic activity. Also plays a role in the regulation of spermatogenesis; inhibits apoptotic activity in spermatogonia.<ref>PMID:18953687</ref> <ref>PMID:22624035</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+RHBDL4 is an active rhomboid that specifically recognizes and cleaves atypical, positively charged transmembrane endoplasmic reticulum-associated degradation (ERAD) substrates. Interaction of valosin-containing protein (p97/VCP) and RHBDL4 is crucial to retrotranslocate polyubiquitinated substrates for ERAD pathway. Here, we report the first complex structure of VCP-binding motif (VBM) with p97 N-terminal domain (p97N) at 1.88 A resolution. Consistent with p97 adaptor proteins including p47-ubiquitin regulatory X (UBX), gp78-VCP-interacting motif (VIM), OTU1-UBX-like element, and FAF1-UBX, RHBDL4 VBM also binds at the interface between the two lobes of p97N. Notably, the RF residues in VBM are involved in the interaction with p97N, showing a similar interaction pattern with that of FPR signature motif in the UBX domain, although the directionality is opposite. Comparison of VBM interaction with VIM of gp78, another alpha-helical motif that interacts with p97N, revealed that the helix direction is inversed. Nevertheless, the conserved arginine residues in both motifs participate in the majority of the interface via extensive hydrogen bonds and ionic interactions with p97N. We identified novel VBM-binding mode to p97N that involves a combination of two types of p97-cofactor specificities observed in the UBX and VIM interactions. This highlights the induced fit model of p97N interdomain cleft upon cofactor binding to form stable p97-cofactor complexes. Our mutational and biochemical analyses in defining the specific interaction between VBM and p97N have elucidated the importance of the highly conserved VBM, applicable to other VBM-containing proteins. We also showed that RHBDL4, ubiquitins, and p97 co-operate for efficient substrate dislocation.
-Authors: Lim, J.J., Ly, T.T., Lee, Y., Kang, J.Y., Lee, J.-G., An, J.Y., Youn, H.-S., Park, K.R., Kim, T.G., Jun, Y., Yang, J.K., Eom, S.H.
+Structural insights into the interaction of p97 N-terminus domain and VBM in rhomboid protease, RHBDL4.,Lim JJ, Lee Y, Ly TT, Kang JY, Lee JG, An JY, Youn HS, Park KR, Kim TG, Yang JK, Jun Y, Eom SH Biochem J. 2016 Sep 15;473(18):2863-80. doi: 10.1042/BCJ20160237. Epub 2016 Jul, 12. PMID:27407164<ref>PMID:27407164</ref>
-Description: Crystal structure of P97 N-terminal domain in complex with a helix
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Youn, H.-S]]
+<div class="pdbe-citations 5epp" style="background-color:#fffaf0;"></div>
-[[Category: Kim, T.G]]
+== References ==
-[[Category: Ly, T.T]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Vesicle-fusing ATPase]]
+[[Category: An, J Y]]
+[[Category: Eom, S H]]
 [[Category: Jun, Y]]
-[[Category: Lim, J.J]]
+[[Category: Kang, J Y]]
-[[Category: Eom, S.H]]
+[[Category: Kim, T G]]
-[[Category: An, J.Y]]
+[[Category: Lee, J G]]
-[[Category: Yang, J.K]]
-[[Category: Park, K.R]]
-[[Category: Kang, J.Y]]
-[[Category: Lee, J.-G]]
 [[Category: Lee, Y]]
+[[Category: Lim, J J]]
+[[Category: Ly, T T]]
+[[Category: Park, K R]]
+[[Category: Yang, J K]]
+[[Category: Youn, H S]]
+[[Category: Atpase]]
+[[Category: Beta-barrel]]
+[[Category: Hydrolase]]
+[[Category: Rhbdl4 vbm motif]]
+[[Category: Ubiquitin]]