2k07

From Proteopedia

(Difference between revisions)

Current revision

Solution NMR structure of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1). Northeast Structural Genomics Consortium target HR41

Structural highlights

2k07 is a 1 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 1ywz. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

UFC1_HUMAN E2-like enzyme which forms an intermediate with UFM1 via a thioester linkage.^[1]

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

For cell regulation, E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1) is involved in the transfer of ubiquitin-fold modifier 1 (Ufm1), a ubiquitin like protein which is activated by E1-like enzyme Uba5, to various target proteins. Thereby, Ufc1 participates in the very recently discovered Ufm1-Uba5-Ufc1 ubiquination pathway which is found in metazoan organisms. The structure of human Ufc1 was solved by using both NMR spectroscopy and X-ray crystallography. The complementary insights obtained with the two techniques provided a unique basis for understanding the function of Ufc1 at atomic resolution. The Ufc1 structure consists of the catalytic core domain conserved in all E2-like enzymes and an additional N-terminal helix. The active site Cys(116), which forms a thio-ester bond with Ufm1, is located in a flexible loop that is highly solvent accessible. Based on the Ufc1 and Ufm1 NMR structures, a model could be derived for the Ufc1-Ufm1 complex in which the C-terminal Gly(83) of Ufm1 may well form the expected thio-ester with Cys(116), suggesting that Ufm1-Ufc1 functions as described for other E1-E2-E3 machineries. alpha-helix 1 of Ufc1 adopts different conformations in the crystal and in solution, suggesting that this helix plays a key role to mediate specificity.

NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway.,Liu G, Forouhar F, Eletsky A, Atreya HS, Aramini JM, Xiao R, Huang YJ, Abashidze M, Seetharaman J, Liu J, Rost B, Acton T, Montelione GT, Hunt JF, Szyperski T J Struct Funct Genomics. 2009 Apr;10(2):127-36. Epub 2008 Dec 20. PMID:19101823^[2]

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

References

↑ Komatsu M, Chiba T, Tatsumi K, Iemura S, Tanida I, Okazaki N, Ueno T, Kominami E, Natsume T, Tanaka K. A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier. EMBO J. 2004 May 5;23(9):1977-86. Epub 2004 Apr 8. PMID:15071506 doi:http://dx.doi.org/10.1038/sj.emboj.7600205
↑ Liu G, Forouhar F, Eletsky A, Atreya HS, Aramini JM, Xiao R, Huang YJ, Abashidze M, Seetharaman J, Liu J, Rost B, Acton T, Montelione GT, Hunt JF, Szyperski T. NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway. J Struct Funct Genomics. 2009 Apr;10(2):127-36. Epub 2008 Dec 20. PMID:19101823 doi:10.1007/s10969-008-9054-7

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/2k07"

@@ Line 1: / Line 1: @@
 ==Solution NMR structure of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1). Northeast Structural Genomics Consortium target HR41==
-<StructureSection load='2k07' size='340' side='right' caption='[[2k07]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2k07' size='340' side='right'caption='[[2k07]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2k07]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ywz 1ywz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K07 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K07 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2k07]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ywz 1ywz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K07 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K07 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UFC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2k07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k07 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2k07 RCSB], [http://www.ebi.ac.uk/pdbsum/2k07 PDBsum], [http://www.topsan.org/Proteins/NESGC/2k07 TOPSAN]</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=2k07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k07 OCA], [https://pdbe.org/2k07 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k07 RCSB], [https://www.ebi.ac.uk/pdbsum/2k07 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k07 ProSAT], [https://www.topsan.org/Proteins/NESGC/2k07 TOPSAN]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UFC1_HUMAN UFC1_HUMAN] E2-like enzyme which forms an intermediate with UFM1 via a thioester linkage.<ref>PMID:15071506</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/k0/2k07_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k0/2k07_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=2k07 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2k07" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ubiquitin-fold modifier 3D structures|Ubiquitin-fold modifier 3D structures]]
 == References ==
 <references/>
@@ Line 29: / Line 36: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Acton, T.]]
+[[Category: Large Structures]]
-[[Category: Aramini, J M.]]
+[[Category: Acton T]]
-[[Category: Atreya, H S.]]
+[[Category: Aramini JM]]
-[[Category: Eletsky, A.]]
+[[Category: Atreya HS]]
-[[Category: Liu, G.]]
+[[Category: Eletsky A]]
-[[Category: Montelione, G T.]]
+[[Category: Liu G]]
-[[Category: NESG, Northeast Structural Genomics Consortium.]]
+[[Category: Montelione GT]]
-[[Category: Szyperski, T.]]
+[[Category: Szyperski T]]
-[[Category: Xiao, R.]]
+[[Category: Xiao R]]
-[[Category: E2]]
-[[Category: Nesg]]
-[[Category: Northeast structural genomics consortium]]
-[[Category: Protein structure initiative]]
-[[Category: Psi-2]]
-[[Category: Structural genomic]]
-[[Category: Ubiquitin conjugating enzyme]]
-[[Category: Ubl conjugation pathway]]
-[[Category: Ufc1]]
-[[Category: Ufm1]]
-[[Category: Unknown function]]

2k07

From Proteopedia

Current revision

Solution NMR structure of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1). Northeast Structural Genomics Consortium target HR41

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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