3m10: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
<StructureSection load='3m10' size='340' side='right'caption='[[3m10]], [[Resolution|resolution]] 1.73Å' scene=''> | <StructureSection load='3m10' size='340' side='right'caption='[[3m10]], [[Resolution|resolution]] 1.73Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3m10]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3m10]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Limulus_polyphemus Limulus polyphemus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1m80 1m80]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M10 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M10 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.727Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3m10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m10 OCA], [https://pdbe.org/3m10 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m10 RCSB], [https://www.ebi.ac.uk/pdbsum/3m10 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m10 ProSAT]</span></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=3m10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m10 OCA], [https://pdbe.org/3m10 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m10 RCSB], [https://www.ebi.ac.uk/pdbsum/3m10 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m10 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/KARG_LIMPO KARG_LIMPO] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 36: | Line 37: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Chapman | [[Category: Limulus polyphemus]] | ||
[[Category: Clark | [[Category: Chapman MS]] | ||
[[Category: Ellington | [[Category: Clark SA]] | ||
[[Category: Pruett | [[Category: Ellington WR]] | ||
[[Category: Somasundaram | [[Category: Pruett PK]] | ||
[[Category: Yousef | [[Category: Somasundaram T]] | ||
[[Category: Yousef MS]] | |||
Latest revision as of 11:46, 6 September 2023
Substrate-free form of Arginine KinaseSubstrate-free form of Arginine Kinase
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe phosphagen kinase family, including creatine and arginine kinases (AKs), catalyzes the reversible transfer of a "high-energy" phosphate between ATP and a phosphoguanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of AK structures were interpreted as a plastic deformation. Here, the structure of Limulus substrate-free AK is refined against high-resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa) and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 A resolution substrate-free crystal structure against the 1.7 A transition-state analog complex shows large substrate-induced domain motions that can be broken down into movements of smaller quasi-rigid bodies. The solution-state structure of substrate-free AK is most consistent with an equilibrium of substrate-free and substrate-bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, "substrate-induced" motions are along modes that are intrinsically flexible in the substrate-free enzyme and likely involve some degree of conformational selection. Arginine kinase: joint crystallographic and NMR RDC analyses link substrate-associated motions to intrinsic flexibility.,Niu X, Bruschweiler-Li L, Davulcu O, Skalicky JJ, Bruschweiler R, Chapman MS J Mol Biol. 2011 Jan 14;405(2):479-96. Epub 2010 Nov 12. PMID:21075117[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||