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[[Image:1kmj.gif|left|200px]]


{{Structure
==E. coli NifS/CsdB protein at 2.0A with the cysteine persulfide intermediate (residue CSS).==
|PDB= 1kmj |SIZE=350|CAPTION= <scene name='initialview01'>1kmj</scene>, resolution 2.0&Aring;
<StructureSection load='1kmj' size='340' side='right'caption='[[1kmj]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=PLP:PYRIDOXAL-5'-PHOSPHATE'>PLP</scene>
<table><tr><td colspan='2'>[[1kmj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KMJ FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Selenocysteine_lyase Selenocysteine lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.16 4.4.1.16]  
</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&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></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=1kmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmj OCA], [https://pdbe.org/1kmj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kmj RCSB], [https://www.ebi.ac.uk/pdbsum/1kmj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kmj ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1kmj TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SUFS_ECOLI SUFS_ECOLI] Cysteine desulfurases mobilize the sulfur from L-cysteine to yield L-alanine, an essential step in sulfur metabolism for biosynthesis of a variety of sulfur-containing biomolecules. Component of the suf operon, which is activated and required under specific conditions such as oxidative stress and iron limitation. Acts as a potent selenocysteine lyase in vitro, that mobilizes selenium from L-selenocysteine. Selenocysteine lyase activity is however unsure in vivo.<ref>PMID:10829016</ref> <ref>PMID:12089140</ref> <ref>PMID:11997471</ref> <ref>PMID:12876288</ref> <ref>PMID:12941942</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/km/1kmj_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=1kmj ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Escherichia coli NifS CsdB protein is a member of the homodimeric pyridoxal 5'-phosphate (PLP)-dependent family of enzymes. These enzymes are capable of decomposing cysteine or selenocysteine into L-alanine and sulfur or selenium, respectively. E. coli NifS CsdB has a high specificity for L-selenocysteine in comparison to l-cysteine, suggesting a role for this enzyme is selenium metabolism. The 2.0 A crystal structure of E. coli NifS CsdB reveals a high-resolution view of the active site of this enzyme in apo-, persulfide, perselenide, and selenocysteine-bound intermediates, suggesting a mechanism for the stabilization of the enzyme persulfide and perselenide intermediates during catalysis, a necessary intermediate in the formation of sulfur and selenium containing metabolites.


'''E. coli NifS/CsdB protein at 2.0A with the cysteine persulfide intermediate (residue CSS).'''
Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation.,Lima CD J Mol Biol. 2002 Feb 1;315(5):1199-208. PMID:11827487<ref>PMID:11827487</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1kmj" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
E2 enzymes catalyze attachment of ubiquitin and ubiquitin-like proteins to lysine residues directly or through E3-mediated reactions. The small ubiquitin-like modifier SUMO regulates nuclear transport, stress response, and signal transduction in eukaryotes and is essential for cell-cycle progression in yeast. In contrast to most ubiquitin conjugation, the SUMO E2 enzyme Ubc9 is sufficient for substrate recognition and lysine modification of known SUMO targets. Crystallographic analysis of a complex between mammalian Ubc9 and a C-terminal domain of RanGAP1 at 2.5 A reveals structural determinants for recognition of consensus SUMO modification sequences found within SUMO-conjugated proteins. Structure-based mutagenesis and biochemical analysis of Ubc9 and RanGAP1 reveal distinct motifs required for substrate binding and SUMO modification of p53, IkappaBalpha, and RanGAP1.
*[[Selenocysteine lyase|Selenocysteine lyase]]
 
== References ==
==About this Structure==
<references/>
1KMJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMJ OCA].
__TOC__
 
</StructureSection>
==Reference==
Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1., Bernier-Villamor V, Sampson DA, Matunis MJ, Lima CD, Cell. 2002 Feb 8;108(3):345-56. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11853669 11853669]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Selenocysteine lyase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Burley SK]]
[[Category: Burley, S K.]]
[[Category: Lima CD]]
[[Category: Lima, C D.]]
[[Category: NYSGXRC, New York Structural GenomiX Research Consortium.]]
[[Category: PLP]]
[[Category: new york structural genomix research consortium]]
[[Category: nysgxrc]]
[[Category: persulfide perselenide nifs pyridoxal phosphate]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: structural genomic]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:19:24 2008''

Latest revision as of 12:01, 16 August 2023

E. coli NifS/CsdB protein at 2.0A with the cysteine persulfide intermediate (residue CSS).E. coli NifS/CsdB protein at 2.0A with the cysteine persulfide intermediate (residue CSS).

Structural highlights

1kmj is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

SUFS_ECOLI Cysteine desulfurases mobilize the sulfur from L-cysteine to yield L-alanine, an essential step in sulfur metabolism for biosynthesis of a variety of sulfur-containing biomolecules. Component of the suf operon, which is activated and required under specific conditions such as oxidative stress and iron limitation. Acts as a potent selenocysteine lyase in vitro, that mobilizes selenium from L-selenocysteine. Selenocysteine lyase activity is however unsure in vivo.[1] [2] [3] [4] [5]

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 Escherichia coli NifS CsdB protein is a member of the homodimeric pyridoxal 5'-phosphate (PLP)-dependent family of enzymes. These enzymes are capable of decomposing cysteine or selenocysteine into L-alanine and sulfur or selenium, respectively. E. coli NifS CsdB has a high specificity for L-selenocysteine in comparison to l-cysteine, suggesting a role for this enzyme is selenium metabolism. The 2.0 A crystal structure of E. coli NifS CsdB reveals a high-resolution view of the active site of this enzyme in apo-, persulfide, perselenide, and selenocysteine-bound intermediates, suggesting a mechanism for the stabilization of the enzyme persulfide and perselenide intermediates during catalysis, a necessary intermediate in the formation of sulfur and selenium containing metabolites.

Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation.,Lima CD J Mol Biol. 2002 Feb 1;315(5):1199-208. PMID:11827487[6]

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

See Also

References

  1. ↑ Lacourciere GM, Mihara H, Kurihara T, Esaki N, Stadtman TC. Escherichia coli NifS-like proteins provide selenium in the pathway for the biosynthesis of selenophosphate. J Biol Chem. 2000 Aug 4;275(31):23769-73. PMID:10829016 doi:10.1074/jbc.M000926200
  2. ↑ Takahashi Y, Tokumoto U. A third bacterial system for the assembly of iron-sulfur clusters with homologs in archaea and plastids. J Biol Chem. 2002 Aug 9;277(32):28380-3. Epub 2002 Jun 27. PMID:12089140 doi:http://dx.doi.org/10.1074/jbc.C200365200
  3. ↑ Mihara H, Kato S, Lacourciere GM, Stadtman TC, Kennedy RA, Kurihara T, Tokumoto U, Takahashi Y, Esaki N. The iscS gene is essential for the biosynthesis of 2-selenouridine in tRNA and the selenocysteine-containing formate dehydrogenase H. Proc Natl Acad Sci U S A. 2002 May 14;99(10):6679-83. Epub 2002 May 7. PMID:11997471 doi:http://dx.doi.org/10.1073/pnas.102176099
  4. ↑ Loiseau L, Ollagnier-de-Choudens S, Nachin L, Fontecave M, Barras F. Biogenesis of Fe-S cluster by the bacterial Suf system: SufS and SufE form a new type of cysteine desulfurase. J Biol Chem. 2003 Oct 3;278(40):38352-9. Epub 2003 Jul 21. PMID:12876288 doi:http://dx.doi.org/10.1074/jbc.M305953200
  5. ↑ Outten FW, Wood MJ, Munoz FM, Storz G. The SufE protein and the SufBCD complex enhance SufS cysteine desulfurase activity as part of a sulfur transfer pathway for Fe-S cluster assembly in Escherichia coli. J Biol Chem. 2003 Nov 14;278(46):45713-9. Epub 2003 Aug 26. PMID:12941942 doi:http://dx.doi.org/10.1074/jbc.M308004200
  6. ↑ Lima CD. Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation. J Mol Biol. 2002 Feb 1;315(5):1199-208. PMID:11827487 doi:10.1006/jmbi.2001.5308

1kmj, resolution 2.00Å

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