5ekn

From Proteopedia

(Difference between revisions)

Revision as of 09:13, 1 November 2017

Crystal structure of MAPK13 complex with inhibitor

Structural highlights

5ekn is a 1 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	4yno, 4myg, 4eyj, 4eym, 5eko
Gene:	MAPK13, PRKM13, SAPK4 (HUMAN)
Activity:	Mitogen-activated protein kinase, with EC number 2.7.11.24
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[MK13_HUMAN] Serine/threonine kinase which acts as an essential component of the MAP kinase signal transduction pathway. MAPK13 is one of the four p38 MAPKs which play an important role in the cascades of cellular responses evoked by extracellular stimuli such as proinflammatory cytokines or physical stress leading to direct activation of transcription factors such as ELK1 and ATF2. Accordingly, p38 MAPKs phosphorylate a broad range of proteins and it has been estimated that they may have approximately 200 to 300 substrates each. MAPK13 is one of the less studied p38 MAPK isoforms. Some of the targets are downstream kinases such as MAPKAPK2, which are activated through phosphorylation and further phosphorylate additional targets. Plays a role in the regulation of protein translation by phosphorylating and inactivating EEF2K. Involved in cytoskeletal remodeling through phosphorylation of MAPT and STMN1. Mediates UV irradiation induced up-regulation of the gene expression of CXCL14. Plays an important role in the regulation of epidermal keratinocyte differentiation, apoptosis and skin tumor development. Phosphorylates the transcriptional activator MYB in response to stress which leads to rapid MYB degradation via a proteasome-dependent pathway. MAPK13 also phosphorylates and down-regulates PRKD1 during regulation of insulin secretion in pancreatic beta cells.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

Publication Abstract from PubMed

BACKGROUND: P38 MAP kinases are centrally involved in mediating extracellular signaling in various diseases. While much attention has previously been focused on the ubiquitously expressed family member MAPK14 (p38alpha), recent studies indicate that family members such as MAPK13 (p38delta) display a more selective cellular and tissue expression and might therefore represent a specific kinase to target in certain diseases. METHODS: To facilitate the design of potent and specific inhibitors, we present here the structural, biophysical, and functional characterization of two new MAPK13-inhibitor complexes, as well as the first comprehensive structural, biophysical, and functional analysis of MAPK13 complexes with four different inhibitor compounds of greatly varying potency. RESULTS: These inhibitors display IC50 values either in the nanomolar range or micromolar range (>800-fold range). The nanomolar inhibitors exhibit much longer ligand-enzyme complex half-lives compared to the micromolar inhibitors as measured by biolayer interferometry. Crystal structures of the MAPK13 inhibitor complexes reveal that the nanomolar inhibitors engage MAPK13 in the DFG-out binding mode, while the micromolar inhibitors are in the DFG-in mode. Detailed structural and computational docking analyses suggest that this difference in binding mode engagement is driven by conformational restraints imposed by the chemical structure of the inhibitors, and may be fortified by an additional hydrogen bond to MAPK13 in the nanomolar inhibitors. CONCLUSIONS: These studies provide a structural basis for understanding the differences in potency exhibited by these inhibitors. GENERAL SIGNIFICANCE: They also provide the groundwork for future studies to improve specificity, potency, pharmacodynamics, and pharmacokinetic properties.

First comprehensive structural and biophysical analysis of MAPK13 inhibitors targeting DFG-in and DFG-out binding modes.,Yurtsever Z, Patel DA, Kober DL, Su A, Miller CA, Romero AG, Holtzman MJ, Brett TJ Biochim Biophys Acta. 2016 Jun 29. pii: S0304-4165(16)30228-8. doi:, 10.1016/j.bbagen.2016.06.023. PMID:27369736^[9]

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

References

↑ Parker CG, Hunt J, Diener K, McGinley M, Soriano B, Keesler GA, Bray J, Yao Z, Wang XS, Kohno T, Lichenstein HS. Identification of stathmin as a novel substrate for p38 delta. Biochem Biophys Res Commun. 1998 Aug 28;249(3):791-6. PMID:9731215 doi:http://dx.doi.org/10.1006/bbrc.1998.9250
↑ Knebel A, Morrice N, Cohen P. A novel method to identify protein kinase substrates: eEF2 kinase is phosphorylated and inhibited by SAPK4/p38delta. EMBO J. 2001 Aug 15;20(16):4360-9. PMID:11500363 doi:http://dx.doi.org/10.1093/emboj/20.16.4360
↑ Buee-Scherrer V, Goedert M. Phosphorylation of microtubule-associated protein tau by stress-activated protein kinases in intact cells. FEBS Lett. 2002 Mar 27;515(1-3):151-4. PMID:11943212
↑ Feijoo C, Campbell DG, Jakes R, Goedert M, Cuenda A. Evidence that phosphorylation of the microtubule-associated protein Tau by SAPK4/p38delta at Thr50 promotes microtubule assembly. J Cell Sci. 2005 Jan 15;118(Pt 2):397-408. Epub 2005 Jan 4. PMID:15632108 doi:http://dx.doi.org/10.1242/jcs.01655
↑ Kraft CA, Efimova T, Eckert RL. Activation of PKCdelta and p38delta MAPK during okadaic acid dependent keratinocyte apoptosis. Arch Dermatol Res. 2007 May;299(2):71-83. Epub 2007 Jan 26. PMID:17256148 doi:http://dx.doi.org/10.1007/s00403-006-0727-4
↑ Pani E, Ferrari S. p38MAPK delta controls c-Myb degradation in response to stress. Blood Cells Mol Dis. 2008 May-Jun;40(3):388-94. Epub 2007 Nov 19. PMID:18006338 doi:http://dx.doi.org/10.1016/j.bcmd.2007.09.010
↑ Zhou X, Ferraris JD, Dmitrieva NI, Liu Y, Burg MB. MKP-1 inhibits high NaCl-induced activation of p38 but does not inhibit the activation of TonEBP/OREBP: opposite roles of p38alpha and p38delta. Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5620-5. doi:, 10.1073/pnas.0801453105. Epub 2008 Mar 26. PMID:18367666 doi:http://dx.doi.org/10.1073/pnas.0801453105
↑ Ozawa S, Ito S, Kato Y, Kubota E, Hata R. Human p38 delta MAP kinase mediates UV irradiation induced up-regulation of the gene expression of chemokine BRAK/CXCL14. Biochem Biophys Res Commun. 2010 Jun 11;396(4):1060-4. doi:, 10.1016/j.bbrc.2010.05.072. Epub 2010 May 15. PMID:20478268 doi:http://dx.doi.org/10.1016/j.bbrc.2010.05.072
↑ Yurtsever Z, Patel DA, Kober DL, Su A, Miller CA, Romero AG, Holtzman MJ, Brett TJ. First comprehensive structural and biophysical analysis of MAPK13 inhibitors targeting DFG-in and DFG-out binding modes. Biochim Biophys Acta. 2016 Jun 29. pii: S0304-4165(16)30228-8. doi:, 10.1016/j.bbagen.2016.06.023. PMID:27369736 doi:http://dx.doi.org/10.1016/j.bbagen.2016.06.023

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/5ekn"

@@ Line 3: / Line 3: @@
 <StructureSection load='5ekn' size='340' side='right' caption='[[5ekn]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ekn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EKN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ekn]] is a 1 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=5EKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EKN FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=N58:1-(3-TERT-BUTYL-1-METHYL-1H-PYRAZOL-5-YL)-3-[4-(PYRIDIN-4-YLSULFANYL)PHENYL]UREA'>N58</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yno|4yno]], [[4myg|4myg]], [[4eyj|4eyj]], [[4eym|4eym]], [[5eko|5eko]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MAPK13, PRKM13, SAPK4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mitogen-activated_protein_kinase Mitogen-activated protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.24 2.7.11.24] </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=5ekn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ekn OCA], [http://pdbe.org/5ekn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ekn RCSB], [http://www.ebi.ac.uk/pdbsum/5ekn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ekn ProSAT]</span></td></tr>
@@ Line 24: / Line 25: @@
 __TOC__
 </StructureSection>
+[[Category: Human]]
 [[Category: Mitogen-activated protein kinase]]
 [[Category: Brett, T J]]

5ekn

From Proteopedia

Revision as of 09:13, 1 November 2017

Crystal structure of MAPK13 complex with inhibitor

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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