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| - | [[Image:1c0n.gif|left|200px]]<br /><applet load="1c0n" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1c0n, resolution 2.8Å" /> | |
| - | '''CSDB PROTEIN, NIFS HOMOLOGUE'''<br /> | |
| | | | |
| - | ==Overview== | + | ==CSDB PROTEIN, NIFS HOMOLOGUE== |
| - | Escherichia coli CsdB, a NifS homologue with a high specificity for, L-selenocysteine, is a pyridoxal 5'-phosphate (PLP)-dependent dimeric, enzyme that belongs to aminotransferases class V in fold-type I of PLP, enzymes and catalyzes the decomposition of L-selenocysteine into selenium, and L-alanine. The crystal structure of the enzyme has been determined by, the X-ray crystallographic method of multiple isomorphous replacement and, refined to an R-factor of 18.7% at 2.8 A resolution. The subunit structure, consists of three parts: a large domain of an alpha/beta-fold containing a, seven-stranded beta-sheet flanked by seven helices, a small domain, containing a four-stranded antiparallel beta-sheet flanked by three, alpha-helices, and an N-terminal segment containing two alpha-helices. The, overall fold of the subunit is similar to those of the enzymes belonging, to the fold-type I family represented by aspartate aminotransferase., However, CsdB has several structural features that are not observed in, other families of the enzymes. A remarkable feature is that an alpha-helix, in the lobe extending from the small domain to the large domain in one, subunit of the dimer interacts with a beta-hairpin loop protruding from, the large domain of the other subunit. The extended lobe and the protruded, beta-hairpin loop form one side of a limb of each active site in the, enzyme. The most striking structural feature of CsdB lies in the location, of a putative catalytic residue; the side chain of Cys364 on the extended, lobe of one subunit is close enough to interact with the gamma-atom of a, modeled substrate in the active site of the subunit. Moreover, His55 from, the other subunit is positioned so that it interacts with the gamma- or, beta-atom of the substrate and may be involved in the catalytic reaction., This is the first report on three-dimensional structures of NifS, homologues. | + | <StructureSection load='1c0n' size='340' side='right'caption='[[1c0n]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1c0n]] 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=1C0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C0N 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=ACY:ACETIC+ACID'>ACY</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=1c0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0n OCA], [https://pdbe.org/1c0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c0n RCSB], [https://www.ebi.ac.uk/pdbsum/1c0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0n 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/c0/1c0n_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1c0n ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Escherichia coli CsdB, a NifS homologue with a high specificity for L-selenocysteine, is a pyridoxal 5'-phosphate (PLP)-dependent dimeric enzyme that belongs to aminotransferases class V in fold-type I of PLP enzymes and catalyzes the decomposition of L-selenocysteine into selenium and L-alanine. The crystal structure of the enzyme has been determined by the X-ray crystallographic method of multiple isomorphous replacement and refined to an R-factor of 18.7% at 2.8 A resolution. The subunit structure consists of three parts: a large domain of an alpha/beta-fold containing a seven-stranded beta-sheet flanked by seven helices, a small domain containing a four-stranded antiparallel beta-sheet flanked by three alpha-helices, and an N-terminal segment containing two alpha-helices. The overall fold of the subunit is similar to those of the enzymes belonging to the fold-type I family represented by aspartate aminotransferase. However, CsdB has several structural features that are not observed in other families of the enzymes. A remarkable feature is that an alpha-helix in the lobe extending from the small domain to the large domain in one subunit of the dimer interacts with a beta-hairpin loop protruding from the large domain of the other subunit. The extended lobe and the protruded beta-hairpin loop form one side of a limb of each active site in the enzyme. The most striking structural feature of CsdB lies in the location of a putative catalytic residue; the side chain of Cys364 on the extended lobe of one subunit is close enough to interact with the gamma-atom of a modeled substrate in the active site of the subunit. Moreover, His55 from the other subunit is positioned so that it interacts with the gamma- or beta-atom of the substrate and may be involved in the catalytic reaction. This is the first report on three-dimensional structures of NifS homologues. |
| | | | |
| - | ==About this Structure==
| + | Structure of a NifS homologue: X-ray structure analysis of CsdB, an Escherichia coli counterpart of mammalian selenocysteine lyase.,Fujii T, Maeda M, Mihara H, Kurihara T, Esaki N, Hata Y Biochemistry. 2000 Feb 15;39(6):1263-73. PMID:10684605<ref>PMID:10684605</ref> |
| - | 1C0N 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 PLP and ACY as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1C0N OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | Structure of a NifS homologue: X-ray structure analysis of CsdB, an Escherichia coli counterpart of mammalian selenocysteine lyase., Fujii T, Maeda M, Mihara H, Kurihara T, Esaki N, Hata Y, Biochemistry. 2000 Feb 15;39(6):1263-73. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10684605 10684605]
| + | </div> |
| - | [[Category: Escherichia coli]]
| + | <div class="pdbe-citations 1c0n" style="background-color:#fffaf0;"></div> |
| - | [[Category: Single protein]]
| + | |
| - | [[Category: Esaki, N.]]
| + | |
| - | [[Category: Fujii, T.]]
| + | |
| - | [[Category: Hata, Y.]]
| + | |
| - | [[Category: Kurihara, T.]]
| + | |
| - | [[Category: Maeda, M.]]
| + | |
| - | [[Category: Mihara, H.]]
| + | |
| - | [[Category: ACY]]
| + | |
| - | [[Category: PLP]]
| + | |
| - | [[Category: alpha/beta fold]]
| + | |
| | | | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:04:05 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: Maeda M]] |
| | + | [[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, a NifS homologue with a high specificity for L-selenocysteine, is a pyridoxal 5'-phosphate (PLP)-dependent dimeric enzyme that belongs to aminotransferases class V in fold-type I of PLP enzymes and catalyzes the decomposition of L-selenocysteine into selenium and L-alanine. The crystal structure of the enzyme has been determined by the X-ray crystallographic method of multiple isomorphous replacement and refined to an R-factor of 18.7% at 2.8 A resolution. The subunit structure consists of three parts: a large domain of an alpha/beta-fold containing a seven-stranded beta-sheet flanked by seven helices, a small domain containing a four-stranded antiparallel beta-sheet flanked by three alpha-helices, and an N-terminal segment containing two alpha-helices. The overall fold of the subunit is similar to those of the enzymes belonging to the fold-type I family represented by aspartate aminotransferase. However, CsdB has several structural features that are not observed in other families of the enzymes. A remarkable feature is that an alpha-helix in the lobe extending from the small domain to the large domain in one subunit of the dimer interacts with a beta-hairpin loop protruding from the large domain of the other subunit. The extended lobe and the protruded beta-hairpin loop form one side of a limb of each active site in the enzyme. The most striking structural feature of CsdB lies in the location of a putative catalytic residue; the side chain of Cys364 on the extended lobe of one subunit is close enough to interact with the gamma-atom of a modeled substrate in the active site of the subunit. Moreover, His55 from the other subunit is positioned so that it interacts with the gamma- or beta-atom of the substrate and may be involved in the catalytic reaction. This is the first report on three-dimensional structures of NifS homologues.
Structure of a NifS homologue: X-ray structure analysis of CsdB, an Escherichia coli counterpart of mammalian selenocysteine lyase.,Fujii T, Maeda M, Mihara H, Kurihara T, Esaki N, Hata Y Biochemistry. 2000 Feb 15;39(6):1263-73. PMID:10684605[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
- ↑ Fujii T, Maeda M, Mihara H, Kurihara T, Esaki N, Hata Y. Structure of a NifS homologue: X-ray structure analysis of CsdB, an Escherichia coli counterpart of mammalian selenocysteine lyase. Biochemistry. 2000 Feb 15;39(6):1263-73. PMID:10684605
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