5fny: Difference between revisions

Latest revision as of 07:00, 19 July 2023

Low solvent content crystal form of Zn containing Iron sulfur cluster repair protein YtfE

Structural highlights

5fny is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.01Å
Ligands:	2PE, FE, O, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YTFE_ECOLI Di-iron-containing protein involved in the repair of iron-sulfur clusters damaged by oxidative and nitrosative stress conditions.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Molecular mechanisms underlying the repair of nitrosylated [Fe-S] clusters by the microbial protein YtfE remain poorly understood. The X-ray crystal structure of YtfE, in combination with EPR, magnetic circular dichroism (MCD), UV, and 17 O-labeling electron spin echo envelope modulation measurements, show that each iron of the oxo-bridged FeII -FeIII diiron core is coordinatively unsaturated with each iron bound to two bridging carboxylates and two terminal histidines in addition to an oxo-bridge. Structural analysis reveals that there are two solvent-accessible tunnels, both of which converge to the diiron center and are critical for capturing substrates. The reactivity of the reduced-form FeII -FeII YtfE toward nitric oxide demonstrates that the prerequisite for N2 O production requires the two iron sites to be nitrosylated simultaneously. Specifically, the nitrosylation of the two iron sites prior to their reductive coupling to produce N2 O is cooperative. This result suggests that, in addition to any repair of iron centers (RIC) activity, YtfE acts as an NO-trapping scavenger to promote the NO to N2 O transformation under low NO flux, which precedes nitrosative stress.

Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO.,Lo FC, Hsieh CC, Maestre-Reyna M, Chen CY, Ko TP, Horng YC, Lai YC, Chiang YW, Chou CM, Chiang CH, Huang WN, Lin YH, Bohle DS, Liaw WF Chemistry. 2016 Jun 1. doi: 10.1002/chem.201600990. PMID:27246459^[4]

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

References

↑ Justino MC, Almeida CC, Goncalves VL, Teixeira M, Saraiva LM. Escherichia coli YtfE is a di-iron protein with an important function in assembly of iron-sulphur clusters. FEMS Microbiol Lett. 2006 Apr;257(2):278-84. PMID:16553864 doi:https://dx.doi.org/10.1111/j.1574-6968.2006.00179.x
↑ Justino MC, Almeida CC, Teixeira M, Saraiva LM. Escherichia coli di-iron YtfE protein is necessary for the repair of stress-damaged iron-sulfur clusters. J Biol Chem. 2007 Apr 6;282(14):10352-9. Epub 2007 Feb 7. PMID:17289666 doi:https://dx.doi.org/10.1074/jbc.M610656200
↑ Todorovic S, Justino MC, Wellenreuther G, Hildebrandt P, Murgida DH, Meyer-Klaucke W, Saraiva LM. Iron-sulfur repair YtfE protein from Escherichia coli: structural characterization of the di-iron center. J Biol Inorg Chem. 2008 Jun;13(5):765-70. doi: 10.1007/s00775-008-0362-y. Epub, 2008 Mar 21. PMID:18357473 doi:https://dx.doi.org/10.1007/s00775-008-0362-y
↑ Lo FC, Hsieh CC, Maestre-Reyna M, Chen CY, Ko TP, Horng YC, Lai YC, Chiang YW, Chou CM, Chiang CH, Huang WN, Lin YH, Bohle DS, Liaw WF. Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO. Chemistry. 2016 Jun 1. doi: 10.1002/chem.201600990. PMID:27246459 doi:https://dx.doi.org/10.1002/chem.201600990

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Justino MC, Almeida CC, Goncalves VL, Teixeira M, Saraiva LM. Escherichia coli YtfE is a di-iron protein with an important function in assembly of iron-sulphur clusters. FEMS Microbiol Lett. 2006 Apr;257(2):278-84. PMID:16553864 doi:https://dx.doi.org/10.1111/j.1574-6968.2006.00179.x

[2] Justino MC, Almeida CC, Teixeira M, Saraiva LM. Escherichia coli di-iron YtfE protein is necessary for the repair of stress-damaged iron-sulfur clusters. J Biol Chem. 2007 Apr 6;282(14):10352-9. Epub 2007 Feb 7. PMID:17289666 doi:https://dx.doi.org/10.1074/jbc.M610656200

[3] Todorovic S, Justino MC, Wellenreuther G, Hildebrandt P, Murgida DH, Meyer-Klaucke W, Saraiva LM. Iron-sulfur repair YtfE protein from Escherichia coli: structural characterization of the di-iron center. J Biol Inorg Chem. 2008 Jun;13(5):765-70. doi: 10.1007/s00775-008-0362-y. Epub, 2008 Mar 21. PMID:18357473 doi:https://dx.doi.org/10.1007/s00775-008-0362-y

[4] Lo FC, Hsieh CC, Maestre-Reyna M, Chen CY, Ko TP, Horng YC, Lai YC, Chiang YW, Chou CM, Chiang CH, Huang WN, Lin YH, Bohle DS, Liaw WF. Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO. Chemistry. 2016 Jun 1. doi: 10.1002/chem.201600990. PMID:27246459 doi:https://dx.doi.org/10.1002/chem.201600990

[1]

[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='5fny' size='340' side='right'caption='[[5fny]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5fny]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FNY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FNY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5fny]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FNY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.01&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5fnn|5fnn]], [[5fnp|5fnp]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_reductase_(cytochrome_c) Nitric-oxide reductase (cytochrome c)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.5 1.7.2.5] </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=5fny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fny OCA], [https://pdbe.org/5fny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fny RCSB], [https://www.ebi.ac.uk/pdbsum/5fny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fny ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5fny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fny OCA], [http://pdbe.org/5fny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fny RCSB], [http://www.ebi.ac.uk/pdbsum/5fny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fny ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/YTFE_ECOLI YTFE_ECOLI]] Di-iron-containing protein involved in the repair of iron-sulfur clusters damaged by oxidative and nitrosative stress conditions.<ref>PMID:16553864</ref> <ref>PMID:17289666</ref> <ref>PMID:18357473</ref>
+[https://www.uniprot.org/uniprot/YTFE_ECOLI YTFE_ECOLI] Di-iron-containing protein involved in the repair of iron-sulfur clusters damaged by oxidative and nitrosative stress conditions.<ref>PMID:16553864</ref> <ref>PMID:17289666</ref> <ref>PMID:18357473</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Chen, C Y]]
+[[Category: Chen C-Y]]
-[[Category: Chiang, C H]]
+[[Category: Chiang C-H]]
-[[Category: Chiang, Y W]]
+[[Category: Chiang Y-W]]
-[[Category: Chou, C M]]
+[[Category: Chou C-M]]
-[[Category: Horng, Y C]]
+[[Category: Horng Y-C]]
-[[Category: Hsieh, C C]]
+[[Category: Hsieh C-C]]
-[[Category: Huang, W N]]
+[[Category: Huang W-N]]
-[[Category: Ko, T P]]
+[[Category: Ko T-P]]
-[[Category: Lai, Y C]]
+[[Category: Lai Y-C]]
-[[Category: Liaw, W F]]
+[[Category: Liaw W-F]]
-[[Category: Lo, F C]]
+[[Category: Lo F-C]]
-[[Category: Maestre-Reyna, M]]
+[[Category: Maestre-Reyna M]]
-[[Category: Di-fe center]]
-[[Category: Iron-sulfur cluster repair]]
-[[Category: Nitric oxide]]
-[[Category: Oxidoreductase]]

5fny: Difference between revisions

Latest revision as of 07:00, 19 July 2023

Low solvent content crystal form of Zn containing Iron sulfur cluster repair protein YtfE

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools