2keo

From Proteopedia

(Difference between revisions)

Revision as of 10:22, 18 July 2018

Solution NMR structure of human protein HS00059, cytochrome-b5-like domain of the HERC2 E3 ligase. Northeast structural genomics consortium (NESG) target ht98a

Structural highlights

2keo is a 1 chain structure with sequence from Human. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	HERC2 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[HERC2_HUMAN] E3 ubiquitin-protein ligase that regulates ubiquitin-dependent retention of repair proteins on damaged chromosomes. Recruited to sites of DNA damage in response to ionizing radiation (IR) and facilitates the assembly of UBE2N and RNF8 promoting DNA damage-induced formation of 'Lys-63'-linked ubiquitin chains. Acts as a mediator of binding specificity between UBE2N and RNF8. Involved in the maintenance of RNF168 levels. E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of XPA which influences the circadian oscillation of DNA excision repair activity.^[1] ^[2] ^[3]

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 quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution - especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

A novel strategy for NMR resonance assignment and protein structure determination.,Lemak A, Gutmanas A, Chitayat S, Karra M, Fares C, Sunnerhagen M, Arrowsmith CH J Biomol NMR. 2011 Jan;49(1):27-38. Epub 2010 Dec 14. PMID:21161328^[4]

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

References

↑ Bekker-Jensen S, Danielsen JR, Fugger K, Gromova I, Nerstedt A, Bartek J, Lukas J, Mailand N. HERC2 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Nat Cell Biol. 2010 Jan;12(1):80-6; sup pp 1-12. Epub 2009 Dec 20. PMID:20023648 doi:ncb2008
↑ Kang TH, Lindsey-Boltz LA, Reardon JT, Sancar A. Circadian control of XPA and excision repair of cisplatin-DNA damage by cryptochrome and HERC2 ubiquitin ligase. Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):4890-5. doi:, 10.1073/pnas.0915085107. PMID:20304803 doi:10.1073/pnas.0915085107
↑ Danielsen JR, Povlsen LK, Villumsen BH, Streicher W, Nilsson J, Wikstrom M, Bekker-Jensen S, Mailand N. DNA damage-inducible SUMOylation of HERC2 promotes RNF8 binding via a novel SUMO-binding Zinc finger. J Cell Biol. 2012 Apr 16;197(2):179-87. doi: 10.1083/jcb.201106152. PMID:22508508 doi:10.1083/jcb.201106152
↑ Lemak A, Gutmanas A, Chitayat S, Karra M, Fares C, Sunnerhagen M, Arrowsmith CH. A novel strategy for NMR resonance assignment and protein structure determination. J Biomol NMR. 2011 Jan;49(1):27-38. Epub 2010 Dec 14. PMID:21161328 doi:10.1007/s10858-010-9458-0

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Solution NMR structure of human protein HS00059, cytochrome-b5-like domain of the HERC2 E3 ligase. Northeast structural genomics consortium (NESG) target ht98a==
 <StructureSection load='2keo' size='340' side='right' caption='[[2keo]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
@@ Line 4: / Line 5: @@
 <table><tr><td colspan='2'>[[2keo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KEO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KEO FirstGlance]. <br>
 </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HERC2 ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2keo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2keo OCA], [http://pdbe.org/2keo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2keo RCSB], [http://www.ebi.ac.uk/pdbsum/2keo PDBsum], [http://www.topsan.org/Proteins/NESGC/2keo TOPSAN]</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=2keo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2keo OCA], [http://pdbe.org/2keo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2keo RCSB], [http://www.ebi.ac.uk/pdbsum/2keo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2keo ProSAT], [http://www.topsan.org/Proteins/NESGC/2keo TOPSAN]</span></td></tr>
 </table>
 == Function ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ke/2keo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ke/2keo_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=2keo ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

2keo

From Proteopedia

Revision as of 10:22, 18 July 2018

Solution NMR structure of human protein HS00059, cytochrome-b5-like domain of the HERC2 E3 ligase. Northeast structural genomics consortium (NESG) target ht98a

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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