1wr0

From Proteopedia

(Difference between revisions)

Current revision

Structural characterization of the MIT domain from human Vps4b

Structural highlights

1wr0 is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

VPS4B_HUMAN Involved in late steps of the endosomal multivesicular bodies (MVB) pathway. Recognizes membrane-associated ESCRT-III assemblies and catalyzes their disassembly, possibly in combination with membrane fission. Redistributes the ESCRT-III components to the cytoplasm for further rounds of MVB sorting. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. In conjunction with the ESCRT machinery also appears to function in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and enveloped virus budding (HIV-1 and other lentiviruses).^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The microtubule interacting and trafficking (MIT) domain is a small protein module of unknown function that is conserved in proteins of diverse function, such as Vps4, sorting nexin 15 (SNX15), and spastin. One non-synonymous single nucleotide polymorphism was reported, which results in a Ile58-to-Met (I58M) substitution in hVps4b. Here, we have determined the solution structure of the MIT domain isolated from the NH(2)-terminus of human Vps4b, an AAA-ATPase involved in multivesicular body formation. The MIT domain adopts an 'up-and-down' three-helix bundle. Comparison with the sequences of other MIT domains clearly shows that the residues involved in inter-helical contacts are well conserved. The Ile58-to-Met substitution resulted a substantial thermal instability. In addition, we found a shallow crevice between helices A and C that may serve as a protein-binding site. We propose that the MIT domain serves as a putative adaptor domain for the ESCRT-III complex involved in endosomal trafficking.

Structural characterization of the MIT domain from human Vps4b.,Takasu H, Jee JG, Ohno A, Goda N, Fujiwara K, Tochio H, Shirakawa M, Hiroaki H Biochem Biophys Res Commun. 2005 Aug 26;334(2):460-5. PMID:16018968^[4]

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

References

↑ Scheuring S, Rohricht RA, Schoning-Burkhardt B, Beyer A, Muller S, Abts HF, Kohrer K. Mammalian cells express two VPS4 proteins both of which are involved in intracellular protein trafficking. J Mol Biol. 2001 Sep 21;312(3):469-80. PMID:11563910 doi:10.1006/jmbi.2001.4917
↑ von Schwedler UK, Stuchell M, Muller B, Ward DM, Chung HY, Morita E, Wang HE, Davis T, He GP, Cimbora DM, Scott A, Krausslich HG, Kaplan J, Morham SG, Sundquist WI. The protein network of HIV budding. Cell. 2003 Sep 19;114(6):701-13. PMID:14505570
↑ Lata S, Schoehn G, Jain A, Pires R, Piehler J, Gottlinger HG, Weissenhorn W. Helical structures of ESCRT-III are disassembled by VPS4. Science. 2008 Sep 5;321(5894):1354-7. doi: 10.1126/science.1161070. Epub 2008 Aug, 7. PMID:18687924 doi:10.1126/science.1161070
↑ Takasu H, Jee JG, Ohno A, Goda N, Fujiwara K, Tochio H, Shirakawa M, Hiroaki H. Structural characterization of the MIT domain from human Vps4b. Biochem Biophys Res Commun. 2005 Aug 26;334(2):460-5. PMID:16018968 doi:10.1016/j.bbrc.2005.06.110

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1wr0"

@@ Line 1: / Line 1: @@
-[[Image:1wr0.gif|left|200px]]<br />
-<applet load="1wr0" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1wr0" />
-'''Structural characterization of the MIT domain from human Vps4b'''<br />
-==Overview==
+==Structural characterization of the MIT domain from human Vps4b==
-The microtubule interacting and trafficking (MIT) domain is a small, protein module of unknown function that is conserved in proteins of, diverse function, such as Vps4, sorting nexin 15 (SNX15), and spastin. One, non-synonymous single nucleotide polymorphism was reported, which results, in a Ile58-to-Met (I58M) substitution in hVps4b. Here, we have determined, the solution structure of the MIT domain isolated from the NH(2)-terminus, of human Vps4b, an AAA-ATPase involved in multivesicular body formation., The MIT domain adopts an 'up-and-down' three-helix bundle. Comparison with, the sequences of other MIT domains clearly shows that the residues, involved in inter-helical contacts are well conserved. The Ile58-to-Met, substitution resulted a substantial thermal instability. In addition, we, found a shallow crevice between helices A and C that may serve as a, protein-binding site. We propose that the MIT domain serves as a putative, adaptor domain for the ESCRT-III complex involved in endosomal, trafficking.
+<StructureSection load='1wr0' size='340' side='right'caption='[[1wr0]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1wr0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WR0 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1wr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wr0 OCA], [https://pdbe.org/1wr0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wr0 RCSB], [https://www.ebi.ac.uk/pdbsum/1wr0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wr0 ProSAT], [https://www.topsan.org/Proteins/RSGI/1wr0 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VPS4B_HUMAN VPS4B_HUMAN] Involved in late steps of the endosomal multivesicular bodies (MVB) pathway. Recognizes membrane-associated ESCRT-III assemblies and catalyzes their disassembly, possibly in combination with membrane fission. Redistributes the ESCRT-III components to the cytoplasm for further rounds of MVB sorting. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. In conjunction with the ESCRT machinery also appears to function in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and enveloped virus budding (HIV-1 and other lentiviruses).<ref>PMID:11563910</ref> <ref>PMID:14505570</ref> <ref>PMID:18687924</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wr/1wr0_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wr0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The microtubule interacting and trafficking (MIT) domain is a small protein module of unknown function that is conserved in proteins of diverse function, such as Vps4, sorting nexin 15 (SNX15), and spastin. One non-synonymous single nucleotide polymorphism was reported, which results in a Ile58-to-Met (I58M) substitution in hVps4b. Here, we have determined the solution structure of the MIT domain isolated from the NH(2)-terminus of human Vps4b, an AAA-ATPase involved in multivesicular body formation. The MIT domain adopts an 'up-and-down' three-helix bundle. Comparison with the sequences of other MIT domains clearly shows that the residues involved in inter-helical contacts are well conserved. The Ile58-to-Met substitution resulted a substantial thermal instability. In addition, we found a shallow crevice between helices A and C that may serve as a protein-binding site. We propose that the MIT domain serves as a putative adaptor domain for the ESCRT-III complex involved in endosomal trafficking.
-==About this Structure==
+Structural characterization of the MIT domain from human Vps4b.,Takasu H, Jee JG, Ohno A, Goda N, Fujiwara K, Tochio H, Shirakawa M, Hiroaki H Biochem Biophys Res Commun. 2005 Aug 26;334(2):460-5. PMID:16018968<ref>PMID:16018968</ref>
-WR0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WR0 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural characterization of the MIT domain from human Vps4b., Takasu H, Jee JG, Ohno A, Goda N, Fujiwara K, Tochio H, Shirakawa M, Hiroaki H, Biochem Biophys Res Commun. 2005 Aug 26;334(2):460-5. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16018968 16018968]
+</div>
-[[Category: Homo sapiens]]
+<div class="pdbe-citations 1wr0" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
-[[Category: Fujiwara, K.]]
-[[Category: Goda, N.]]
-[[Category: Hiroaki, H.]]
-[[Category: Jee, J.G.]]
-[[Category: Ohno, A.]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
-[[Category: Shirakawa, M.]]
-[[Category: Takasu, H.]]
-[[Category: Tochio, H.]]
-[[Category: escort]]
-[[Category: mit domain]]
-[[Category: mvb]]
-[[Category: national project on protein structural and functional analyses]]
-[[Category: nppsfa]]
-[[Category: protein transport]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rsgi]]
-[[Category: skd1]]
-[[Category: snps]]
-[[Category: structural genomics]]
-[[Category: vps4b]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 19:53:54 2007''
+==See Also==
+*[[Vacuolar protein sorting-associated protein 3D structures|Vacuolar protein sorting-associated protein 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Fujiwara K]]
+[[Category: Goda N]]
+[[Category: Hiroaki H]]
+[[Category: Jee JG]]
+[[Category: Ohno A]]
+[[Category: Shirakawa M]]
+[[Category: Takasu H]]
+[[Category: Tochio H]]

1wr0

From Proteopedia

Current revision

Structural characterization of the MIT domain from human Vps4b

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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