4lve

From Proteopedia

(Difference between revisions)

Current revision

LEN K30T MUTANT: A DOMAIN FLIP AS A RESULT OF A SINGLE AMINO ACID SUBSTITUTION

Structural highlights

4lve is a 2 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 2.3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KV401_HUMAN V segment of the variable domain of immunoglobulins light chain that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:22158414, PubMed:20176268). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:20176268, PubMed:17576170).^[1] ^[2] ^[3] ^[4]

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

BACKGROUND: The self-assembly properties of beta domains are important features of diverse classes of proteins that include cell-adhesion molecules, surface receptors and the immunoglobulin superfamily. Immunoglobulin light-chain variable domains are well suited to the study of structural factors that determine dimerization, including how residues at the interface influence the preferred dimer arrangement. RESULTS: Single-site mutants of light-chain variable domain Len, designated LenQ38E and LenK30T, formed 'flipped' dimers in which one domain was rotated by about 180 degrees compared with the native protein. The dimer in the native protein is similar to that found between variable domains in Fab immunoglobulin fragments. When compared to the native dimer, more surface area is buried, and more hydrogen bonds and salt bridges are formed between the monomers in the flipped conformation. CONCLUSIONS: Immunoglobulin light-chain variable domains can form a minimum of two distinct quaternary structures. Single-site mutations resulting from changes of one base, such as the exchange of Gln38 to Glu or Lys30 to Thr, change the 'conventional' dimer of protein Len to a flipped arrangement. Native Len is not found in the flipped-domain dimer conformation because it would have excess positive electrostatic potential at the dimer interface that is not compensated by other forces. Excess negative or positive electrostatic potential at the dimer interface can have a determining effect on the mode of dimerization.

A domain flip as a result of a single amino-acid substitution.,Pokkuluri PR, Huang DB, Raffen R, Cai X, Johnson G, Stevens PW, Stevens FJ, Schiffer M Structure. 1998 Aug 15;6(8):1067-73. PMID:9739086^[5]

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

References

↑ Teng G, Papavasiliou FN. Immunoglobulin somatic hypermutation. Annu Rev Genet. 2007;41:107-20. PMID:17576170 doi:http://dx.doi.org/10.1146/annurev.genet.41.110306.130340
↑ Schroeder HW Jr, Cavacini L. Structure and function of immunoglobulins. J Allergy Clin Immunol. 2010 Feb;125(2 Suppl 2):S41-52. doi:, 10.1016/j.jaci.2009.09.046. PMID:20176268 doi:http://dx.doi.org/10.1016/j.jaci.2009.09.046
↑ McHeyzer-Williams M, Okitsu S, Wang N, McHeyzer-Williams L. Molecular programming of B cell memory. Nat Rev Immunol. 2011 Dec 9;12(1):24-34. doi: 10.1038/nri3128. PMID:22158414 doi:http://dx.doi.org/10.1038/nri3128
↑ Lefranc MP. Immunoglobulin and T Cell Receptor Genes: IMGT((R)) and the Birth and Rise of Immunoinformatics. Front Immunol. 2014 Feb 5;5:22. doi: 10.3389/fimmu.2014.00022. eCollection 2014. PMID:24600447 doi:http://dx.doi.org/10.3389/fimmu.2014.00022
↑ Pokkuluri PR, Huang DB, Raffen R, Cai X, Johnson G, Stevens PW, Stevens FJ, Schiffer M. A domain flip as a result of a single amino-acid substitution. Structure. 1998 Aug 15;6(8):1067-73. PMID:9739086

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4lve"

Categories: Homo sapiens | Large Structures | Pokkuluri PR | Schiffer M

@@ Line 1: / Line 1: @@
 ==LEN K30T MUTANT: A DOMAIN FLIP AS A RESULT OF A SINGLE AMINO ACID SUBSTITUTION==
-<StructureSection load='4lve' size='340' side='right' caption='[[4lve]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='4lve' size='340' side='right'caption='[[4lve]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4lve]] is a 2 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=4LVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LVE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4lve]] 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=4LVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LVE FirstGlance]. <br>
-</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=4lve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lve OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lve RCSB], [http://www.ebi.ac.uk/pdbsum/4lve PDBsum]</span></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]] 2.3&#8491;</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=4lve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lve OCA], [https://pdbe.org/4lve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lve RCSB], [https://www.ebi.ac.uk/pdbsum/4lve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lve ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/KV401_HUMAN KV401_HUMAN] V segment of the variable domain of immunoglobulins light chain that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:22158414, PubMed:20176268). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:20176268, PubMed:17576170).<ref>PMID:17576170</ref> <ref>PMID:20176268</ref> <ref>PMID:22158414</ref> <ref>PMID:24600447</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/lv/4lve_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lv/4lve_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=4lve ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 23: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4lve" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 28: / Line 33: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Pokkuluri, P R]]
+[[Category: Large Structures]]
-[[Category: Schiffer, M]]
+[[Category: Pokkuluri PR]]
-[[Category: Immunoglobulin]]
+[[Category: Schiffer M]]
-[[Category: Kappa-iv]]
-[[Category: Light chain dimer]]

4lve

From Proteopedia

Current revision

LEN K30T MUTANT: A DOMAIN FLIP AS A RESULT OF A SINGLE AMINO ACID SUBSTITUTION

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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