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4nxr

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Revision as of 10:02, 21 December 2022

Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Neurexin-1 Peptide

Structural highlights

4nxr 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.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TIAM1_HUMAN Modulates the activity of RHO-like proteins and connects extracellular signals to cytoskeletal activities. Acts as a GDP-dissociation stimulator protein that stimulates the GDP-GTP exchange activity of RHO-like GTPases and activates them. Activates RAC1, CDC42, and to a lesser extent RHOA.

Publication Abstract from PubMed

Conformational dynamics has an established role in enzyme catalysis, but its contribution to ligand binding and specificity is largely unexplored. Here we used the Tiam1 PDZ domain and an engineered variant (QM PDZ) with broadened specificity to investigate the role of structure and conformational dynamics in molecular recognition. Crystal structures of the QM PDZ domain both free and bound to ligands showed structural features central to binding (enthalpy), while nuclear-magnetic-resonance-based methyl relaxation experiments and isothermal titration calorimetry revealed that conformational entropy contributes to affinity. In addition to motions relevant to thermodynamics, slower microsecond to millisecond switching was prevalent in the QM PDZ ligand-binding site consistent with a role in ligand specificity. Our data indicate that conformational dynamics plays distinct and fundamental roles in tuning the affinity (conformational entropy) and specificity (excited-state conformations) of molecular interactions. More broadly, our results have important implications for the evolution, regulation, and design of protein-ligand interactions.

Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions.,Liu X, Speckhard DC, Shepherd TR, Sun YJ, Hengel SR, Yu L, Fowler CA, Gakhar L, Fuentes EJ Structure. 2016 Dec 6;24(12):2053-2066. doi: 10.1016/j.str.2016.08.019. Epub 2016, Oct 27. PMID:27998539^[1]

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

References

↑ Liu X, Speckhard DC, Shepherd TR, Sun YJ, Hengel SR, Yu L, Fowler CA, Gakhar L, Fuentes EJ. Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions. Structure. 2016 Dec 6;24(12):2053-2066. doi: 10.1016/j.str.2016.08.019. Epub 2016, Oct 27. PMID:27998539 doi:http://dx.doi.org/10.1016/j.str.2016.08.019

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='4nxr' size='340' side='right'caption='[[4nxr]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4nxr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NXR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NXR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4nxr]] 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=4NXR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NXR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANS:5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC+ACID(DANSYL+ACID)'>ANS</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANS:5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC+ACID(DANSYL+ACID)'>ANS</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kzd|3kzd]], [[3kze|3kze]], [[4gvd|4gvd]], [[4gvc|4gvc]], [[4nxq|4nxq]], [[4nxp|4nxp]]</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=4nxr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nxr OCA], [https://pdbe.org/4nxr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nxr RCSB], [https://www.ebi.ac.uk/pdbsum/4nxr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nxr ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TIAM1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4nxr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nxr OCA], [http://pdbe.org/4nxr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nxr RCSB], [http://www.ebi.ac.uk/pdbsum/4nxr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nxr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TIAM1_HUMAN TIAM1_HUMAN]] Modulates the activity of RHO-like proteins and connects extracellular signals to cytoskeletal activities. Acts as a GDP-dissociation stimulator protein that stimulates the GDP-GTP exchange activity of RHO-like GTPases and activates them. Activates RAC1, CDC42, and to a lesser extent RHOA. [[http://www.uniprot.org/uniprot/NRX2B_HUMAN NRX2B_HUMAN]] Neuronal cell surface protein that may be involved in cell recognition and cell adhesion.
+[https://www.uniprot.org/uniprot/TIAM1_HUMAN TIAM1_HUMAN] Modulates the activity of RHO-like proteins and connects extracellular signals to cytoskeletal activities. Acts as a GDP-dissociation stimulator protein that stimulates the GDP-GTP exchange activity of RHO-like GTPases and activates them. Activates RAC1, CDC42, and to a lesser extent RHOA.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Fuentes, E J]]
+[[Category: Fuentes EJ]]
-[[Category: Hengel, S R]]
+[[Category: Hengel SR]]
-[[Category: Liu, X]]
+[[Category: Liu X]]
-[[Category: Shepherd, T R]]
+[[Category: Shepherd TR]]
-[[Category: Speckhard, D C]]
+[[Category: Speckhard DC]]
-[[Category: Beta barrel fold protein]]
-[[Category: Pdz domain]]
-[[Category: Peptide binding]]
-[[Category: Scaffold signaling protein for cell adhesion and cell junction]]
-[[Category: Signaling domain]]
-[[Category: Signaling protein-peptide complex]]
-[[Category: Specificity mutant]]

4nxr

From Proteopedia

Revision as of 10:02, 21 December 2022

Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Neurexin-1 Peptide

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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