3m10

From Proteopedia

(Difference between revisions)

Revision as of 04:04, 10 December 2016

Substrate-free form of Arginine Kinase

Structural highlights

3m10 is a 2 chain structure with sequence from Atlantic horseshoe crab. This structure supersedes the now removed PDB entry 1m80. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1m80, 1m15
Activity:	Arginine kinase, with EC number 2.7.3.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

The 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.

References

↑ Niu X, Bruschweiler-Li L, Davulcu O, Skalicky JJ, Bruschweiler R, Chapman MS. Arginine kinase: joint crystallographic and NMR RDC analyses link substrate-associated motions to intrinsic flexibility. J Mol Biol. 2011 Jan 14;405(2):479-96. Epub 2010 Nov 12. PMID:21075117 doi:10.1016/j.jmb.2010.11.007

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3m10"

@@ Line 1: / Line 1: @@
 ==Substrate-free form of Arginine Kinase==
 <StructureSection load='3m10' size='340' side='right' caption='[[3m10]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3m10]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M10 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3m10]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atlantic_horseshoe_crab Atlantic horseshoe crab]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M10 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1m80|1m80]], [[1m15|1m15]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_kinase Arginine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.3.3 2.7.3.3] </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=3m10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m10 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m10 RCSB], [http://www.ebi.ac.uk/pdbsum/3m10 PDBsum]</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=3m10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m10 OCA], [http://pdbe.org/3m10 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3m10 RCSB], [http://www.ebi.ac.uk/pdbsum/3m10 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3m10 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 16: / Line 17: @@
     <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=3m10 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3m10" style="background-color:#fffaf0;"></div>
 ==See Also==
+*[[Arginine Kinase AK|Arginine Kinase AK]]
+*[[Arginine kinase|Arginine kinase]]
 *[[Transthyretin|Transthyretin]]
 == References ==
@@ Line 34: / Line 38: @@
 </StructureSection>
 [[Category: Arginine kinase]]
-[[Category: Limulus polyphemus]]
+[[Category: Atlantic horseshoe crab]]
 [[Category: Chapman, M S]]
 [[Category: Clark, S A]]

3m10

From Proteopedia

Revision as of 04:04, 10 December 2016

Substrate-free form of Arginine Kinase

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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