User:Olivier Laprevote/Sandbox 1

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==Proto-oncogene vav==
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=Proto-oncogene vav=
<StructureSection load='3ky9' size='340' side='right' caption='Caption for this structure' scene='75/751211/Monomerous_vav/1'>
<StructureSection load='3ky9' size='340' side='right' caption='Caption for this structure' scene='75/751211/Monomerous_vav/1'>
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This is a default text for your page '''Olivier Laprevote/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
 
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You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
 
== Function ==
== Function ==
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Vav1 is a '''Guanine Exchange Factor''' (GEF) for the Rho/Rac protein family <ref> http://mcb.asm.org/content/20/5/1461.full </ref>.
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Vav1 is a '''Guanine Exchange Factor''' (GEF) for the <scene name='75/751211/Vav_rac/1'>Rho/Rac protein family</scene> <ref> http://mcb.asm.org/content/20/5/1461.full </ref>.
It is involved in cellular response to external stimuli, by inducing cytoskeletal rearrangement or by inter-mediating pathways cascades. As such, the '''proto-oncogene''' encoded Vav1 protein has a role in growth and division of the cell, but also in apoptotic pathways.
It is involved in cellular response to external stimuli, by inducing cytoskeletal rearrangement or by inter-mediating pathways cascades. As such, the '''proto-oncogene''' encoded Vav1 protein has a role in growth and division of the cell, but also in apoptotic pathways.
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Vav1 is mainly found in hematopoietic cells <ref> http://www.proteinatlas.org/ENSG00000141968-VAV1/tissue </ref> and is involved in the '''differentiation''' of T lymphocytes, then in B and T cells '''development''' and '''maturation''' <ref> PMID:14623913 </ref>.
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Vav1 also has a role in Ca2+ induced signalling pathways in immune response of B and T cells.
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Vav1 is mainly found in hematopoietic cells <ref> http://www.proteinatlas.org/ENSG00000141968-VAV1/tissue </ref> and is involved in the '''differentiation''' of T lymphocytes, then in B and T cells '''development''' and '''maturation''' <ref> PMID:14623913 </ref>. Vav1 also has a role in Ca2+ induced signalling pathways in immune response of B and T cells.
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HIV-1 Nef protein has been found to bind specifically to Vav1, affecting its nucleus-to-cytoplasm distribution, and thus delaying the immune reaction <ref> PMID:14597672 </ref>
HIV-1 Nef protein has been found to bind specifically to Vav1, affecting its nucleus-to-cytoplasm distribution, and thus delaying the immune reaction <ref> PMID:14597672 </ref>
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== Disease relevance ==
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VAV1 is often considered a potentially prooncogenic protein since anormal VAV1 was proved to be involved in many cases of mammalian malignancies, including neuroblastoma, melanoma, pancreatic, lung and breast cancers<ref>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4745688/</ref>. What's more, it's also often found to be overexpressed in cancer cells whereas it's usually only expressed in the hematopoietic system. VAV1 is indeed involved in many pathways that ultimalty lead to the regulation of the activity of several transcription factors that play a major role in the regulation of cell apoptosis or cell proliferation, such as NF-AT<ref>http://www.nature.com/onc/journal/v20/n44/full/1204780a.html</ref> or Rac1, PAK1, and NF-κB that causes cyclin D1 upregulation<ref>http://www.cell.com/cancer-cell/abstract/S1535-6108(04)00370-8</ref>. It's still unknown if mutations take part in the cell proliferation effect. What has been confirmed though, is that mere epigenetic modifications could contribute to it. Furthermore, VAV1 is implicated in other immune system related pathways. Studies showed that VAV1 deficient organisms had a slower immune response to infections. No diseases have been found out though that was involving such a feature of VAV1<ref>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485565/</ref>.
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== Disease Relevance ==
 
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The major reason why VAV1 is a protein of interest is because it was revealed that many mutants are often implicated in numerous cases of cancer such as implicated in mammalian malignancies, including neuroblastoma, melanoma, pancreatic, lung and breast cancers, and B-cell chronic lymphocytic leukemia and it's frequently overexpressed in tumors whereas it's normally solely expressed in the hematopoietic system . As a regulatory protein, it's involved in many pathways that end up controlling the activity of important transcription factors that influence cell cycle regulation. It's been discovered to take part in the NF-AT pathway as well as the Rac1, PAK1, and NF-kappaB and involve cyclin D1 upregulation. That's why it's now considered as a potentially prooncogenic protein. It's still unsure how mutations of VAV1 affect the risks of cancer and it's been demonstrated that epigenetic changes alone contributed to an aberrant proliferation of cells. It was also discovered that a mutation of VAV1 could weaken the immune response of mammalians, however, no immune disability had been reported yet that involved a deficience with VAV1.
 
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== diagnostic and therapeutic context ==
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== Therapeutic context ==
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Although VAV1 has clearly been identified as an oncogenic protein already, there are still very little ways to regulate its activity as a cell proliferation factor. Treatments are being studies for the moment. Studies showed that VAV1 promoter demethylation as an event in cancer progression, suggesting that aberrant signaling pathways driven by VAV1 are potential therapeutic targets in Pancreatic ductal adenocarcinoma<ref>https://www-ncbi-nlm-nih-gov.scd-rproxy.u-strasbg.fr/pubmed/?term=VAV1%3A+a+new+target+in+pancreatic+cancer%3F</ref>. Aside from that, it's also being researched if already known antioncogenic drug would stop VAV1 induced cell proliferation<ref>http://cancerres.aacrjournals.org/content/75/14/2907</ref>.
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== Structural highlights ==
== Structural highlights ==
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Src-homology domains SH3-SH2-SH3 (residues 617 - 842): the activators of Vav like Syk or ZP-70 fix on its SH2 region <ref>PMID: 9850860</ref>. Potential inhibitors of Vav also dock on its SH3-SH2-SH3 region, such as SHP which would remove the phosphate on Y174 <ref>PMID: 8632004</ref> or Cbl-b <ref>PMID: 9399639</ref>. It has also been proven that the C-ter SH3 was involved in the auto-inhibition of Vav. <ref>PMID: 24736456  </ref>
Src-homology domains SH3-SH2-SH3 (residues 617 - 842): the activators of Vav like Syk or ZP-70 fix on its SH2 region <ref>PMID: 9850860</ref>. Potential inhibitors of Vav also dock on its SH3-SH2-SH3 region, such as SHP which would remove the phosphate on Y174 <ref>PMID: 8632004</ref> or Cbl-b <ref>PMID: 9399639</ref>. It has also been proven that the C-ter SH3 was involved in the auto-inhibition of Vav. <ref>PMID: 24736456  </ref>
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== Auto-inhibition and activation ==
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=== Auto-inhibition ===
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When Tyr-174 on the Ac domain is not phosphorylated, Vav1 is auto-inhibited. It has long been thought that only the CH and Ac domain interactions with the DH, PH and C1/ZN domains played a role in auto-inhibition. Indeed, <scene name='75/751211/Ch_ph/2'>CH domain residues 66-68 interact with the PH domain residues 406-408</scene>, forming beta-sheet like hydrogen bonds. There is also a <scene name='75/751211/Ph_ac/1'>close interaction between the PH and Ac domains</scene>interaction between the PH and Ac domains, some oppositely charged residues facing each other like Asp-150 on Ac and Lys-487 on PH.
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These interactions seem to strengthen the formation of an inhibitory helix on the Ac domain (residues 167-178) which binds on DH domain and block its access to the substrate. Moreover, the interactions between the PH and CH domains coupled with the interaction of the latter and the N-terminus region of the Ac domain strengthen the helix, so there are two processes involved in Vav auto-inhibition. <ref>PMID: 20141838 </ref>
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When Tyr-174 on the Ac domain is not phosphorylated, Vav1 is auto-inhibited. It has long been thought that only the CH and Ac domain interactions with the DH, PH and C1/ZN domains played a role in auto-inhibition. Indeed, <scene name='75/751211/Ch_ph/2'>CH domain residues 66-68 interact with the PH domain residues 406-408</scene>, forming beta-sheet like hydrogen bonds. There is also a close interaction between the PH and Ac domains, some oppositely charged residues facing each other like Asp-150 on Ac and Lys-487 on PH. <ref>PMID: 20141838 </ref>
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Tyr-541 and Tyr 544 on C1 and Tyr-836 on the C-terminal SH3 domains have also to get phosphorylated in order to activate Vav1, the SH3 domain also binding on the DH (residues 371 – 388) if this tyrosine wasn’t phosphorylated. <ref>PMID:24736456 </ref>
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=== Activation ===
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The phosphorylation of Tyr-174 in vivo happens within seconds after a kinase has bound to Vav1. It induces the deformation of the inhibitory helix, thus et separates itself of the active site of the DH domain. The phosphorylation of Tyr-160 and -142 makes Tyr-174 more accessible as it lessen the interactions between the CH and Acidic domains. <ref>PMID: 20141838 </ref>
== Vav activity ==
== Vav activity ==
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Upon antigen recognition in BCR and TCR pathways, Src family kinases phosphorylate Y174 residue of Vav1. Activated Vav1 can then express its GEF activity on Rac1 <ref> http://www.ebi.ac.uk/intact/interaction/EBI-7944187;jsessionid=8AD6943D454A170511925DF549C751E4 </ref>.
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Upon antigen recognition in BCR and TCR pathways, '''Src family kinases''' phosphorylate Y174 residue of Vav1, so that activated Vav1 can then express its GEF activity on Rac1 <ref> http://www.ebi.ac.uk/intact/interaction/EBI-7944187;jsessionid=8AD6943D454A170511925DF549C751E4 </ref>. The PH domain structures the protein so that DH and C1 are available for Rac1 binding. The C1 domain is rich in cysteine and harbours two Zn fingers involved in the binding of RhoGTPases <ref> PMID:2620086 </ref>.
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Rac1 has two '''switch regions''' that bind to C1 and DH domain. The first switch binds to two highly conserved regions of C1 domain, CR1 (Conserved Region)and CR3. The second switch binds to CR3 and to the C-terminal α-helix of DH domain. These two domains widen the binding cavity to mediate the release of GDP to exchange for GTP <ref> PMID:2620086 </ref>.
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Vav family is atypical for its special C1 domain with Zn fingers. This allows recognition of various RhoGTPases, while GEFs proteins are usually specific to only one.
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<scene name='75/751211/Vav_rac/1'>Vav interacting with Rac</scene>
 

Current revision

Proto-oncogene vav

Caption for this structure

Drag the structure with the mouse to rotate

References

  1. http://mcb.asm.org/content/20/5/1461.full
  2. http://www.proteinatlas.org/ENSG00000141968-VAV1/tissue
  3. Fujikawa K, Miletic AV, Alt FW, Faccio R, Brown T, Hoog J, Fredericks J, Nishi S, Mildiner S, Moores SL, Brugge J, Rosen FS, Swat W. Vav1/2/3-null mice define an essential role for Vav family proteins in lymphocyte development and activation but a differential requirement in MAPK signaling in T and B cells. J Exp Med. 2003 Nov 17;198(10):1595-608. PMID:14623913 doi:http://dx.doi.org/10.1084/jem.20030874
  4. Quaranta MG, Mattioli B, Spadaro F, Straface E, Giordani L, Ramoni C, Malorni W, Viora M. HIV-1 Nef triggers Vav-mediated signaling pathway leading to functional and morphological differentiation of dendritic cells. FASEB J. 2003 Nov;17(14):2025-36. PMID:14597672 doi:http://dx.doi.org/10.1096/fj.03-0272com
  5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4745688/
  6. http://www.nature.com/onc/journal/v20/n44/full/1204780a.html
  7. http://www.cell.com/cancer-cell/abstract/S1535-6108(04)00370-8
  8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485565/
  9. https://www-ncbi-nlm-nih-gov.scd-rproxy.u-strasbg.fr/pubmed/?term=VAV1%3A+a+new+target+in+pancreatic+cancer%3F
  10. http://cancerres.aacrjournals.org/content/75/14/2907
  11. http://smart.embl.de/smart/show_motifs.pl?GENOMIC=1&DO_PFAM=DO_PFAM&INCLUDE_SIGNALP=INCLUDE_SIGNALP&ID=9606.ENSP00000472929
  12. Yu B, Martins IR, Li P, Amarasinghe GK, Umetani J, Fernandez-Zapico ME, Billadeau DD, Machius M, Tomchick DR, Rosen MK. Structural and energetic mechanisms of cooperative autoinhibition and activation of Vav1. Cell. 2010 Jan 22;140(2):246-56. PMID:20141838 doi:10.1016/j.cell.2009.12.033
  13. Llorca O, Arias-Palomo E, Zugaza JL, Bustelo XR. Global conformational rearrangements during the activation of the GDP/GTP exchange factor Vav3. EMBO J. 2005 Apr 6;24(7):1330-40. Epub 2005 Mar 10. PMID:15775967 doi:http://dx.doi.org/10.1038/sj.emboj.7600617
  14. Yu B, Martins IR, Li P, Amarasinghe GK, Umetani J, Fernandez-Zapico ME, Billadeau DD, Machius M, Tomchick DR, Rosen MK. Structural and energetic mechanisms of cooperative autoinhibition and activation of Vav1. Cell. 2010 Jan 22;140(2):246-56. PMID:20141838 doi:10.1016/j.cell.2009.12.033
  15. http://pfam.xfam.org/family/PF00621
  16. Movilla N, Bustelo XR. Biological and regulatory properties of Vav-3, a new member of the Vav family of oncoproteins. Mol Cell Biol. 1999 Nov;19(11):7870-85. PMID:10523675
  17. Han J, Luby-Phelps K, Das B, Shu X, Xia Y, Mosteller RD, Krishna UM, Falck JR, White MA, Broek D. Role of substrates and products of PI 3-kinase in regulating activation of Rac-related guanosine triphosphatases by Vav. Science. 1998 Jan 23;279(5350):558-60. PMID:9438848
  18. Chu DH, Morita CT, Weiss A. The Syk family of protein tyrosine kinases in T-cell activation and development. Immunol Rev. 1998 Oct;165:167-80. PMID:9850860
  19. Kon-Kozlowski M, Pani G, Pawson T, Siminovitch KA. The tyrosine phosphatase PTP1C associates with Vav, Grb2, and mSos1 in hematopoietic cells. J Biol Chem. 1996 Feb 16;271(7):3856-62. PMID:8632004
  20. Bustelo XR, Crespo P, Lopez-Barahona M, Gutkind JS, Barbacid M. Cbl-b, a member of the Sli-1/c-Cbl protein family, inhibits Vav-mediated c-Jun N-terminal kinase activation. Oncogene. 1997 Nov 20;15(21):2511-20. PMID:9399639
  21. PMID: 24736456 
  22. PMID: 20141838
  23. Barreira M, Fabbiano S, Couceiro JR, Torreira E, Martinez-Torrecuadrada JL, Montoya G, Llorca O, Bustelo XR. The C-terminal SH3 domain contributes to the intramolecular inhibition of Vav family proteins. Sci Signal. 2014 Apr 15;7(321):ra35. doi: 10.1126/scisignal.2004993. PMID:24736456 doi:http://dx.doi.org/10.1126/scisignal.2004993
  24. PMID: 20141838
  25. http://www.ebi.ac.uk/intact/interaction/EBI-7944187;jsessionid=8AD6943D454A170511925DF549C751E4
  26. Koutsouris D, Guillet R, Wenby RB, Meiselman HJ. Determination of erythrocyte transit times through micropores. II. Influence of experimental and physicochemical factors. Biorheology. 1989;26(5):881-98. PMID:2620086
  27. Koutsouris D, Guillet R, Wenby RB, Meiselman HJ. Determination of erythrocyte transit times through micropores. II. Influence of experimental and physicochemical factors. Biorheology. 1989;26(5):881-98. PMID:2620086

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