3tw8: Difference between revisions

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==GEF domain of DENND 1B in complex with Rab GTPase Rab35==
==GEF domain of DENND 1B in complex with Rab GTPase Rab35==
<StructureSection load='3tw8' size='340' side='right' caption='[[3tw8]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='3tw8' size='340' side='right'caption='[[3tw8]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3tw8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TW8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TW8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3tw8]] is a 4 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=3TW8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TW8 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2fol|2fol]], [[1yzn|1yzn]]</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]] 2.1&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DENND1B, C1orf218, FAM31B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RAB35, RAB1C, RAY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3tw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tw8 OCA], [https://pdbe.org/3tw8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tw8 RCSB], [https://www.ebi.ac.uk/pdbsum/3tw8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tw8 ProSAT]</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=3tw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tw8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tw8 RCSB], [http://www.ebi.ac.uk/pdbsum/3tw8 PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/DEN1B_HUMAN DEN1B_HUMAN]] Guanine nucleotide exchange factor (GEF) for RAB35. Promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB35 into its active GTP-bound form. May play a role in clathrin-mediated endocytosis.<ref>PMID:20154091</ref> <ref>PMID:20937701</ref> 
[https://www.uniprot.org/uniprot/DEN1B_HUMAN DEN1B_HUMAN] Guanine nucleotide exchange factor (GEF) for RAB35. Promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB35 into its active GTP-bound form. May play a role in clathrin-mediated endocytosis.<ref>PMID:20154091</ref> <ref>PMID:20937701</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Rab GTPases are key regulators of membrane traffic pathways within eukaryotic cells. They are specifically activated by guanine nucleotide exchange factors (GEFs), which convert them from their "inactive" GDP-bound form to the "active" GTP-bound form. In higher eukaryotes, proteins containing DENN-domains comprise a major GEF family. Here we describe at 2.1-A resolution the first structure of a DENN-domain protein, DENND1B-S, complexed with its substrate Rab35, providing novel insights as to how DENN-domain GEFs interact with and activate Rabs. DENND1B-S is bi-lobed, and interactions with Rab35 are through conserved surfaces in both lobes. Rab35 binds via switch regions I and II, around the nucleotide-binding pocket. Positional shifts in Rab residues required for nucleotide binding may lower its affinity for bound GDP, and a conformational change in switch I, which makes the nucleotide-binding pocket more solvent accessible, likely also facilitates exchange.
 
Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate.,Wu X, Bradley MJ, Cai Y, Kummel D, De La Cruz EM, Barr FA, Reinisch KM Proc Natl Acad Sci U S A. 2011 Nov 7. PMID:22065758<ref>PMID:22065758</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[GTP-binding protein|GTP-binding protein]]
*[[GTP-binding protein 3D structures|GTP-binding protein 3D structures]]
*[[Ras-related protein Rab 3D structures|Ras-related protein Rab 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Kummel, D]]
[[Category: Large Structures]]
[[Category: Reinisch, K M]]
[[Category: Kummel D]]
[[Category: Wu, X D]]
[[Category: Reinisch KM]]
[[Category: Guanine exchange factor]]
[[Category: Wu XD]]
[[Category: Longin domain]]
[[Category: Protein transport]]
[[Category: Rab gtpase]]

Latest revision as of 13:15, 1 March 2024

GEF domain of DENND 1B in complex with Rab GTPase Rab35GEF domain of DENND 1B in complex with Rab GTPase Rab35

Structural highlights

3tw8 is a 4 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 2.1Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DEN1B_HUMAN Guanine nucleotide exchange factor (GEF) for RAB35. Promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB35 into its active GTP-bound form. May play a role in clathrin-mediated endocytosis.[1] [2]

See Also

References

  1. ↑ Marat AL, McPherson PS. The connecdenn family, Rab35 guanine nucleotide exchange factors interfacing with the clathrin machinery. J Biol Chem. 2010 Apr 2;285(14):10627-37. doi: 10.1074/jbc.M109.050930. Epub 2010, Feb 12. PMID:20154091 doi:http://dx.doi.org/10.1074/jbc.M109.050930
  2. ↑ Yoshimura S, Gerondopoulos A, Linford A, Rigden DJ, Barr FA. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. J Cell Biol. 2010 Oct 18;191(2):367-81. doi: 10.1083/jcb.201008051. Epub 2010 Oct, 11. PMID:20937701 doi:http://dx.doi.org/10.1083/jcb.201008051

3tw8, resolution 2.10Å

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