2io2: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:


==Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1==
==Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1==
<StructureSection load='2io2' size='340' side='right' caption='[[2io2]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
<StructureSection load='2io2' size='340' side='right'caption='[[2io2]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2io2]] is a 3 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=2IO2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IO2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2io2]] is a 3 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=2IO2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IO2 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tgz|1tgz]], [[2io0|2io0]], [[2io1|2io1]], [[2io3|2io3]]</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]] 2.9&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SENP2, KIAA1331 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), SUMO1, SMT3C, SMT3H3, UBL1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RANGAP1 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=2io2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2io2 OCA], [https://pdbe.org/2io2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2io2 RCSB], [https://www.ebi.ac.uk/pdbsum/2io2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2io2 ProSAT]</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=2io2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2io2 OCA], [http://pdbe.org/2io2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2io2 RCSB], [http://www.ebi.ac.uk/pdbsum/2io2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2io2 ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Defects in SUMO1 are the cause of non-syndromic orofacial cleft type 10 (OFC10) [MIM:[http://omim.org/entry/613705 613705]]; also called non-syndromic cleft lip with or without cleft palate 10. OFC10 is a birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. Note=A chromosomal aberation involving SUMO1 is the cause of OFC10. Translocation t(2;8)(q33.1;q24.3). The breakpoint occurred in the SUMO1 gene and resulted in haploinsufficiency confirmed by protein assays.<ref>PMID:16990542</ref> 
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/SENP2_HUMAN SENP2_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. May down-regulate CTNNB1 levels and thereby modulate the Wnt pathway (By similarity).<ref>PMID:12192048</ref> <ref>PMID:11896061</ref> [[http://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Ubiquitin-like protein that can be covalently attached to proteins as a monomer or a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by E3 ligases such as PIAS1-4, RANBP2 or CBX4. This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Involved for instance in targeting RANGAP1 to the nuclear pore complex protein RANBP2. Polymeric SUMO1 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins. May also regulate a network of genes involved in palate development.<ref>PMID:9019411</ref> <ref>PMID:9162015</ref> <ref>PMID:18538659</ref> <ref>PMID:18408734</ref> 
[https://www.uniprot.org/uniprot/SENP2_HUMAN SENP2_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. May down-regulate CTNNB1 levels and thereby modulate the Wnt pathway (By similarity).<ref>PMID:12192048</ref> <ref>PMID:11896061</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/io/2io2_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/io/2io2_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 31: Line 28:
</div>
</div>
<div class="pdbe-citations 2io2" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 2io2" style="background-color:#fffaf0;"></div>
==See Also==
*[[Sentrin-specific protease|Sentrin-specific protease]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Lima, C D]]
[[Category: Large Structures]]
[[Category: Reverter, D]]
[[Category: Lima CD]]
[[Category: Complex]]
[[Category: Reverter D]]
[[Category: Hydrolase]]
[[Category: Protein binding]]
[[Category: Senp]]
[[Category: Sumo]]
[[Category: Ubiquitin]]
[[Category: Ulp]]

Latest revision as of 13:14, 30 August 2023

Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1

Structural highlights

2io2 is a 3 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 2.9Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SENP2_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. May down-regulate CTNNB1 levels and thereby modulate the Wnt pathway (By similarity).[1] [2]

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

SUMO processing and deconjugation are essential proteolytic activities for nuclear metabolism and cell-cycle progression in yeast and higher eukaryotes. To elucidate the mechanisms used during substrate lysine deconjugation, SUMO isoform processing and SUMO isoform interactions, X-ray structures were determined for a catalytically inert SENP2 protease domain in complex with conjugated RanGAP1-SUMO-1 or RanGAP1-SUMO-2, or in complex with SUMO-2 or SUMO-3 precursors. Common features within the active site include a 90 degrees kink proximal to the scissile bond that forces C-terminal amino acid residues or the lysine side chain toward a protease surface that appears optimized for lysine deconjugation. Analysis of this surface reveals SENP2 residues, particularly Met497, that mediate, and in some instances reverse, in vitro substrate specificity. Mutational analysis and biochemistry provide a mechanism for SENP2 substrate preferences that explains why SENP2 catalyzes SUMO deconjugation more efficiently than processing.

Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates.,Reverter D, Lima CD Nat Struct Mol Biol. 2006 Dec;13(12):1060-8. Epub 2006 Nov 12. PMID:17099700[3]

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

See Also

References

  1. ↑ Zhang H, Saitoh H, Matunis MJ. Enzymes of the SUMO modification pathway localize to filaments of the nuclear pore complex. Mol Cell Biol. 2002 Sep;22(18):6498-508. PMID:12192048
  2. ↑ Hang J, Dasso M. Association of the human SUMO-1 protease SENP2 with the nuclear pore. J Biol Chem. 2002 May 31;277(22):19961-6. Epub 2002 Mar 14. PMID:11896061 doi:10.1074/jbc.M201799200
  3. ↑ Reverter D, Lima CD. Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates. Nat Struct Mol Biol. 2006 Dec;13(12):1060-8. Epub 2006 Nov 12. PMID:17099700 doi:10.1038/nsmb1168

2io2, resolution 2.90Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2io2&oldid=3851927"