2xre

From Proteopedia

(Difference between revisions)

Current revision

Detection of cobalt in previously unassigned human SENP1 structure

Structural highlights

2xre 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 2.45Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SENP1_HUMAN Protease that catalyzes two essential functions in the SUMO pathway: processing of full-length SUMO1, SUMO2 and SUMO3 to their mature forms and deconjugation of SUMO1, SUMO2 and SUMO3 from targeted proteins. Deconjugates SUMO1 from HIPK2. Deconjugates SUMO1 from HDAC1, which decreases its transcriptional repression activity.^[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

Metal ions often stabilize intermolecular contacts between macromolecules, thereby promoting crystallization. When interpreting a medium-resolution electron-density map of the catalytic domain of human sentrin-specific protease 1 (SENP1), a strong feature indicative of an ordered divalent cation was noted. This was assigned as Co(2+), an essential component of the crystallization mixture. The ion displays tetrahedral coordination by Glu430 and His640 from one molecule and the corresponding residues from a symmetry-related molecule. Analysis of the data derived from a previous structure of SENP1 suggested that Co(2+) had been overlooked and re-refinement supported this conclusion. High-throughput automated re-refinement protocols also failed to mark the Co(2+) position, supporting the requirement for the incorporation of as much information as possible to enhance the value of such protocols.

The role of Co(2)+ in the crystallization of human SENP1 and comments on the limitations of automated refinement protocols.,Rimsa V, Eadsforth T, Hunter WN Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Apr 1;67(Pt 4):442-5. Epub, 2011 Mar 24. PMID:21505236^[5]

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

References

↑ Gong L, Millas S, Maul GG, Yeh ET. Differential regulation of sentrinized proteins by a novel sentrin-specific protease. J Biol Chem. 2000 Feb 4;275(5):3355-9. PMID:10652325
↑ Cheng J, Wang D, Wang Z, Yeh ET. SENP1 enhances androgen receptor-dependent transcription through desumoylation of histone deacetylase 1. Mol Cell Biol. 2004 Jul;24(13):6021-8. PMID:15199155 doi:10.1128/MCB.24.13.6021-6028.2004
↑ Kim YH, Sung KS, Lee SJ, Kim YO, Choi CY, Kim Y. Desumoylation of homeodomain-interacting protein kinase 2 (HIPK2) through the cytoplasmic-nuclear shuttling of the SUMO-specific protease SENP1. FEBS Lett. 2005 Nov 7;579(27):6272-8. Epub 2005 Oct 19. PMID:16253240 doi:S0014-5793(05)01251-2
↑ Shen LN, Dong C, Liu H, Naismith JH, Hay RT. The structure of SENP1-SUMO-2 complex suggests a structural basis for discrimination between SUMO paralogues during processing. Biochem J. 2006 Jul 15;397(2):279-88. PMID:16553580 doi:10.1042/BJ20052030
↑ Rimsa V, Eadsforth T, Hunter WN. The role of Co(2)+ in the crystallization of human SENP1 and comments on the limitations of automated refinement protocols. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Apr 1;67(Pt 4):442-5. Epub, 2011 Mar 24. PMID:21505236 doi:10.1107/S1744309111005835

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2xre"

@@ Line 1: / Line 1: @@
 ==Detection of cobalt in previously unassigned human SENP1 structure==
-<StructureSection load='2xre' size='340' side='right' caption='[[2xre]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
+<StructureSection load='2xre' size='340' side='right'caption='[[2xre]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xre]] 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=2XRE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XRE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xre]] 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=2XRE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XRE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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]] 2.45&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2iyd|2iyd]], [[2iyc|2iyc]], [[2iy1|2iy1]], [[2iy0|2iy0]], [[2ckg|2ckg]], [[2xph|2xph]], [[2g4d|2g4d]], [[2ckh|2ckh]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=2xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xre OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xre RCSB], [http://www.ebi.ac.uk/pdbsum/2xre PDBsum]</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=2xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xre OCA], [https://pdbe.org/2xre PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xre RCSB], [https://www.ebi.ac.uk/pdbsum/2xre PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xre ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SENP1_HUMAN SENP1_HUMAN]] Protease that catalyzes two essential functions in the SUMO pathway: processing of full-length SUMO1, SUMO2 and SUMO3 to their mature forms and deconjugation of SUMO1, SUMO2 and SUMO3 from targeted proteins. Deconjugates SUMO1 from HIPK2. Deconjugates SUMO1 from HDAC1, which decreases its transcriptional repression activity.<ref>PMID:10652325</ref> <ref>PMID:15199155</ref> <ref>PMID:16253240</ref> <ref>PMID:16553580</ref>
+[https://www.uniprot.org/uniprot/SENP1_HUMAN SENP1_HUMAN] Protease that catalyzes two essential functions in the SUMO pathway: processing of full-length SUMO1, SUMO2 and SUMO3 to their mature forms and deconjugation of SUMO1, SUMO2 and SUMO3 from targeted proteins. Deconjugates SUMO1 from HIPK2. Deconjugates SUMO1 from HDAC1, which decreases its transcriptional repression activity.<ref>PMID:10652325</ref> <ref>PMID:15199155</ref> <ref>PMID:16253240</ref> <ref>PMID:16553580</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/xr/2xre_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xr/2xre_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=2xre ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2xre" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Eadsforth, T]]
+[[Category: Large Structures]]
-[[Category: Hay, R T]]
+[[Category: Eadsforth T]]
-[[Category: Hunter, W N]]
+[[Category: Hay RT]]
-[[Category: Rimsa, V]]
+[[Category: Hunter WN]]
-[[Category: Cysteine protease]]
+[[Category: Rimsa V]]
-[[Category: Hydrolase]]

2xre

From Proteopedia

Current revision

Detection of cobalt in previously unassigned human SENP1 structure

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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