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| - | [[Image:1i29.gif|left|200px]]<br /><applet load="1i29" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1i29, resolution 2.80Å" /> | |
| - | '''CRYSTAL STRUCTURE OF CSDB COMPLEXED WITH L-PROPARGYLGLYCINE'''<br /> | |
| | | | |
| - | ==Overview== | + | ==CRYSTAL STRUCTURE OF CSDB COMPLEXED WITH L-PROPARGYLGLYCINE== |
| - | Escherichia coli CsdB is a pyridoxal 5'-phosphate (PLP)-dependent enzyme, that catalyzes both cysteine desulfuration and selenocysteine, deselenation. The enzyme has a high specific activity for L-selenocysteine, relative to L-cysteine. On the other hand, its paralog, IscS, exhibits, higher activity for L-cysteine, which acts as a sulfur donor during the, biosynthesis of the iron-sulfur cluster and 4-thiouridine. The structure, of CsdB complexed with L-propargylglycine was determined by X-ray, crystallography at 2.8 A resolution. The overall polypeptide fold of the, complex is similar to that of the uncomplexed enzyme, indicating that no, significant structural change occurs upon formation of the complex. In the, complex, propargylglycine forms a Schiff base with PLP, providing the, features of the external aldimine formed in the active site. The Cys364, residue, which is essential for the activity of CsdB toward L-cysteine but, not toward L-selenocysteine, is clearly visible on a loop of the extended, lobe (Thr362-Arg375) in all enzyme forms studied, in contrast to the, corresponding disordered loop (Ser321-Arg332) of the Thermotoga maritima, NifS-like protein, which is closely related to IscS. The extended lobe of, CsdB has an 11-residue deletion compared with that of the NifS-like, protein. These facts suggest that the restricted flexibility of the, Cys364-anchoring extended lobe in CsdB may be responsible for the ability, of the enzyme to discriminate between selenium and sulfur. | + | <StructureSection load='1i29' size='340' side='right'caption='[[1i29]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1i29]] 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=1I29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I29 FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LPG:L-PROPARGYLGLYCINE'>LPG</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=1i29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i29 OCA], [https://pdbe.org/1i29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i29 RCSB], [https://www.ebi.ac.uk/pdbsum/1i29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i29 ProSAT]</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/i2/1i29_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=1i29 ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Escherichia coli CsdB is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes both cysteine desulfuration and selenocysteine deselenation. The enzyme has a high specific activity for L-selenocysteine relative to L-cysteine. On the other hand, its paralog, IscS, exhibits higher activity for L-cysteine, which acts as a sulfur donor during the biosynthesis of the iron-sulfur cluster and 4-thiouridine. The structure of CsdB complexed with L-propargylglycine was determined by X-ray crystallography at 2.8 A resolution. The overall polypeptide fold of the complex is similar to that of the uncomplexed enzyme, indicating that no significant structural change occurs upon formation of the complex. In the complex, propargylglycine forms a Schiff base with PLP, providing the features of the external aldimine formed in the active site. The Cys364 residue, which is essential for the activity of CsdB toward L-cysteine but not toward L-selenocysteine, is clearly visible on a loop of the extended lobe (Thr362-Arg375) in all enzyme forms studied, in contrast to the corresponding disordered loop (Ser321-Arg332) of the Thermotoga maritima NifS-like protein, which is closely related to IscS. The extended lobe of CsdB has an 11-residue deletion compared with that of the NifS-like protein. These facts suggest that the restricted flexibility of the Cys364-anchoring extended lobe in CsdB may be responsible for the ability of the enzyme to discriminate between selenium and sulfur. |
| | | | |
| - | ==About this Structure==
| + | Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine.,Mihara H, Fujii T, Kato S, Kurihara T, Hata Y, Esaki N J Biochem. 2002 May;131(5):679-85. PMID:11983074<ref>PMID:11983074</ref> |
| - | 1I29 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with LPG and PLP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1I29 OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine., Mihara H, Fujii T, Kato S, Kurihara T, Hata Y, Esaki N, J Biochem (Tokyo). 2002 May;131(5):679-85. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11983074 11983074]
| + | </div> |
| - | [[Category: Escherichia coli]]
| + | <div class="pdbe-citations 1i29" style="background-color:#fffaf0;"></div> |
| - | [[Category: Selenocysteine lyase]]
| + | |
| - | [[Category: Single protein]]
| + | |
| - | [[Category: Esaki, N.]]
| + | |
| - | [[Category: Fujii, T.]]
| + | |
| - | [[Category: Hata, Y.]]
| + | |
| - | [[Category: Kurihara, T.]]
| + | |
| - | [[Category: Mihara, H.]]
| + | |
| - | [[Category: LPG]]
| + | |
| - | [[Category: PLP]]
| + | |
| - | [[Category: external aldimine]]
| + | |
| | | | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 16:59:26 2007''
| + | ==See Also== |
| | + | *[[Selenocysteine lyase|Selenocysteine lyase]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Escherichia coli]] |
| | + | [[Category: Large Structures]] |
| | + | [[Category: Esaki N]] |
| | + | [[Category: Fujii T]] |
| | + | [[Category: Hata Y]] |
| | + | [[Category: Kurihara T]] |
| | + | [[Category: Mihara H]] |
| Structural highlights
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
Escherichia coli CsdB is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes both cysteine desulfuration and selenocysteine deselenation. The enzyme has a high specific activity for L-selenocysteine relative to L-cysteine. On the other hand, its paralog, IscS, exhibits higher activity for L-cysteine, which acts as a sulfur donor during the biosynthesis of the iron-sulfur cluster and 4-thiouridine. The structure of CsdB complexed with L-propargylglycine was determined by X-ray crystallography at 2.8 A resolution. The overall polypeptide fold of the complex is similar to that of the uncomplexed enzyme, indicating that no significant structural change occurs upon formation of the complex. In the complex, propargylglycine forms a Schiff base with PLP, providing the features of the external aldimine formed in the active site. The Cys364 residue, which is essential for the activity of CsdB toward L-cysteine but not toward L-selenocysteine, is clearly visible on a loop of the extended lobe (Thr362-Arg375) in all enzyme forms studied, in contrast to the corresponding disordered loop (Ser321-Arg332) of the Thermotoga maritima NifS-like protein, which is closely related to IscS. The extended lobe of CsdB has an 11-residue deletion compared with that of the NifS-like protein. These facts suggest that the restricted flexibility of the Cys364-anchoring extended lobe in CsdB may be responsible for the ability of the enzyme to discriminate between selenium and sulfur.
Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine.,Mihara H, Fujii T, Kato S, Kurihara T, Hata Y, Esaki N J Biochem. 2002 May;131(5):679-85. PMID:11983074[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ Mihara H, Fujii T, Kato S, Kurihara T, Hata Y, Esaki N. Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine. J Biochem. 2002 May;131(5):679-85. PMID:11983074
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