1ni7

From Proteopedia

(Difference between revisions)

Current revision

NORTHEAST STRUCTURAL GENOMIC CONSORTIUM TARGET ER75

Structural highlights

1ni7 is a 1 chain structure with sequence from Escherichia coli. 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

CSDE_ECOLI Stimulates the cysteine desulfurase activity of CsdA. Contains a cysteine residue (Cys-61) that acts to accept sulfur liberated via the desulfurase activity of CsdA. May be able to transfer sulfur to TcdA/CsdL. Seems to support the function of TcdA in the generation of cyclic threonylcarbamoyladenosine at position 37 (ct(6)A37) in tRNAs that read codons beginning with adenine. Does not appear to participate in Fe/S biogenesis.^[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 structural biology of proteins mediating iron-sulfur (Fe-S) cluster assembly is central for understanding several important biological processes. Here we present the NMR structure of the 16-kDa protein YgdK from Escherichia coli, which shares 35% sequence identity with the E. coli protein SufE. The SufE X-ray crystal structure was solved in parallel with the YdgK NMR structure in the Northeast Structural Genomics (NESG) consortium. Both proteins are (1) key components for Fe-S metabolism, (2) exhibit the same distinct fold, and (3) belong to a family of at least 70 prokaryotic and eukaryotic sequence homologs. Accurate homology models were calculated for the YgdK/SufE family based on YgdK NMR and SufE crystal structure. Both structural templates contributed equally, exemplifying synergy of NMR and X-ray crystallography. SufE acts as an enhancer of the cysteine desulfurase activity of SufS by SufE-SufS complex formation. A homology model of CsdA, a desulfurase encoded in the same operon as YgdK, was modeled using the X-ray structure of SufS as a template. Protein surface and electrostatic complementarities strongly suggest that YgdK and CsdA likewise form a functional two-component desulfurase complex. Moreover, structural features of YgdK and SufS, which can be linked to their interaction with desulfurases, are conserved in all homology models. It thus appears very likely that all members of the YgdK/SufE family act as enhancers of Suf-S-like desulfurases. The present study exemplifies that "refined" selection of two (or more) targets enables high-quality homology modeling of large protein families.

High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.,Liu G, Li Z, Chiang Y, Acton T, Montelione GT, Murray D, Szyperski T Protein Sci. 2005 Jun;14(6):1597-608. PMID:15930006^[4]

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

References

↑ Loiseau L, Ollagnier-de Choudens S, Lascoux D, Forest E, Fontecave M, Barras F. Analysis of the heteromeric CsdA-CsdE cysteine desulfurase, assisting Fe-S cluster biogenesis in Escherichia coli. J Biol Chem. 2005 Jul 22;280(29):26760-9. Epub 2005 May 18. PMID:15901727 doi:http://dx.doi.org/10.1074/jbc.M504067200
↑ Trotter V, Vinella D, Loiseau L, Ollagnier de Choudens S, Fontecave M, Barras F. The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf components and participates to a new sulphur transfer pathway by recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein. Mol Microbiol. 2009 Dec;74(6):1527-42. PMID:20054882
↑ Miyauchi K, Kimura S, Suzuki T. A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol. 2013 Feb;9(2):105-11. doi: 10.1038/nchembio.1137. Epub 2012 Dec, 16. PMID:23242255 doi:http://dx.doi.org/10.1038/nchembio.1137
↑ Liu G, Li Z, Chiang Y, Acton T, Montelione GT, Murray D, Szyperski T. High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases. Protein Sci. 2005 Jun;14(6):1597-608. PMID:15930006 doi:14/6/1597

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/1ni7"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1ni7.png|left|200px]]
-<!--
+==NORTHEAST STRUCTURAL GENOMIC CONSORTIUM TARGET ER75==
-The line below this paragraph, containing "STRUCTURE_1ni7", creates the "Structure Box" on the page.
+<StructureSection load='1ni7' size='340' side='right'caption='[[1ni7]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1ni7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NI7 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1ni7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ni7 OCA], [https://pdbe.org/1ni7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ni7 RCSB], [https://www.ebi.ac.uk/pdbsum/1ni7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ni7 ProSAT], [https://www.topsan.org/Proteins/NESGC/1ni7 TOPSAN]</span></td></tr>
-{{STRUCTURE_1ni7|  PDB=1ni7  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CSDE_ECOLI CSDE_ECOLI] Stimulates the cysteine desulfurase activity of CsdA. Contains a cysteine residue (Cys-61) that acts to accept sulfur liberated via the desulfurase activity of CsdA. May be able to transfer sulfur to TcdA/CsdL. Seems to support the function of TcdA in the generation of cyclic threonylcarbamoyladenosine at position 37 (ct(6)A37) in tRNAs that read codons beginning with adenine. Does not appear to participate in Fe/S biogenesis.<ref>PMID:15901727</ref> <ref>PMID:20054882</ref> <ref>PMID:23242255</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/ni/1ni7_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/main_output.php?pdb_ID=1ni7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structural biology of proteins mediating iron-sulfur (Fe-S) cluster assembly is central for understanding several important biological processes. Here we present the NMR structure of the 16-kDa protein YgdK from Escherichia coli, which shares 35% sequence identity with the E. coli protein SufE. The SufE X-ray crystal structure was solved in parallel with the YdgK NMR structure in the Northeast Structural Genomics (NESG) consortium. Both proteins are (1) key components for Fe-S metabolism, (2) exhibit the same distinct fold, and (3) belong to a family of at least 70 prokaryotic and eukaryotic sequence homologs. Accurate homology models were calculated for the YgdK/SufE family based on YgdK NMR and SufE crystal structure. Both structural templates contributed equally, exemplifying synergy of NMR and X-ray crystallography. SufE acts as an enhancer of the cysteine desulfurase activity of SufS by SufE-SufS complex formation. A homology model of CsdA, a desulfurase encoded in the same operon as YgdK, was modeled using the X-ray structure of SufS as a template. Protein surface and electrostatic complementarities strongly suggest that YgdK and CsdA likewise form a functional two-component desulfurase complex. Moreover, structural features of YgdK and SufS, which can be linked to their interaction with desulfurases, are conserved in all homology models. It thus appears very likely that all members of the YgdK/SufE family act as enhancers of Suf-S-like desulfurases. The present study exemplifies that "refined" selection of two (or more) targets enables high-quality homology modeling of large protein families.
-===NORTHEAST STRUCTURAL GENOMIC CONSORTIUM TARGET ER75===
+High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.,Liu G, Li Z, Chiang Y, Acton T, Montelione GT, Murray D, Szyperski T Protein Sci. 2005 Jun;14(6):1597-608. PMID:15930006<ref>PMID:15930006</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15930006}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ni7" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15930006 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15930006}}
+__TOC__
+</StructureSection>
-==About this Structure==
-NI7 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NI7 OCA].
-==Reference==
-High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases., Liu G, Li Z, Chiang Y, Acton T, Montelione GT, Murray D, Szyperski T, Protein Sci. 2005 Jun;14(6):1597-608. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15930006 15930006]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Acton, T.]]
+[[Category: Acton T]]
-[[Category: Chiang, Y.]]
+[[Category: Chiang Y]]
-[[Category: Liu, G.]]
+[[Category: Liu G]]
-[[Category: Montelione, G T.]]
+[[Category: Montelione GT]]
-[[Category: NESG, Northeast Structural Genomics Consortium.]]
+[[Category: Szyperski T]]
-[[Category: Szyperski, T.]]
-[[Category: Er75]]
-[[Category: Nesg]]
-[[Category: Northeast structural genomics consortium]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Rd-nmr]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 11:11:00 2008''

1ni7

From Proteopedia

Current revision

NORTHEAST STRUCTURAL GENOMIC CONSORTIUM TARGET ER75

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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