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5lmc

From Proteopedia

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Current revision

Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms from its rubredoxin domain

Structural highlights

5lmc is a 1 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 1.9Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NORV_ECOLI Anaerobic nitric oxide reductase; uses NADH to detoxify nitric oxide (NO), protecting several 4Fe-4S NO-sensitive enzymes. Has at least 2 reductase partners, only one of which (NorW, flavorubredoxin reductase) has been identified. NO probably binds to the di-iron center; electrons enter from the reductase at rubredoxin and are transferred sequentially to the FMN center and the di-iron center. Also able to function as an aerobic oxygen reductase.^[1] ^[2]

Publication Abstract from PubMed

Flavodiiron proteins (FDPs) are present in organisms from all domains of life and have been described so far to be involved in the detoxification of oxygen or nitric oxide, acting as O2 and/or NO reductases. The Escherichia coli FDP, named flavorubredoxin (FlRd) is the most extensively studied FDP. Biochemical and in vivo studies revealed that FlRd is involved in NO detoxification, as part of the bacterial defense mechanisms against reactive nitrogen species. E. coli FlRd has a clear preference for NO as substrate in vitro, exhibiting a very low reactivity towards O2. To contribute to the understanding of the structural features defining this substrate selectivity, we determined the crystallographic structure of E. coli FlRd, both in the as-isolated and reduced states. The overall tetrameric structure revealed a highly conserved flavodiiron core domain, with a metallo-beta-lactamase-like domain containing a diiron center and a flavodoxin domain with a FMN cofactor. The metal center in the oxidized state has a mu-hydroxo bridge coordinating the two irons, while in the reduced state this moiety is not detected. Since only the flavodiiron domain was observed in these crystal structures, the structure of the rubredoxin domain was determined by NMR. Tunnels for the substrates were identified, and through Molecular Dynamics simulations no differences for O2 or NO permeation were found. The present data represents the first structure for a NO-selective FDP.

Structure of Escherichia coli Flavodiiron nitric oxide reductase.,Romao CV, Vicente JB, Borges PT, Victor BL, Lamosa P, Silva E, Pereira L, Bandeiras TM, Soares CM, Carrondo MA, Turner D, Teixeira M, Frazao C J Mol Biol. 2016 Oct 7. pii: S0022-2836(16)30423-5. doi:, 10.1016/j.jmb.2016.10.008. PMID:27725182^[3]

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

References

↑ Gardner AM, Helmick RA, Gardner PR. Flavorubredoxin, an inducible catalyst for nitric oxide reduction and detoxification in Escherichia coli. J Biol Chem. 2002 Mar 8;277(10):8172-7. Epub 2001 Dec 18. PMID:11751865 doi:http://dx.doi.org/10.1074/jbc.M110471200
↑ Gomes CM, Giuffre A, Forte E, Vicente JB, Saraiva LM, Brunori M, Teixeira M. A novel type of nitric-oxide reductase. Escherichia coli flavorubredoxin. J Biol Chem. 2002 Jul 12;277(28):25273-6. Epub 2002 May 6. PMID:12101220 doi:http://dx.doi.org/10.1074/jbc.M203886200
↑ Romao CV, Vicente JB, Borges PT, Victor BL, Lamosa P, Silva E, Pereira L, Bandeiras TM, Soares CM, Carrondo MA, Turner D, Teixeira M, Frazao C. Structure of Escherichia coli Flavodiiron nitric oxide reductase. J Mol Biol. 2016 Oct 7. pii: S0022-2836(16)30423-5. doi:, 10.1016/j.jmb.2016.10.008. PMID:27725182 doi:http://dx.doi.org/10.1016/j.jmb.2016.10.008

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5lmc"

@@ Line 1: / Line 1: @@
 ==Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms from its rubredoxin domain==
-<StructureSection load='5lmc' size='340' side='right' caption='[[5lmc]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='5lmc' size='340' side='right'caption='[[5lmc]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5lmc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LMC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5lmc]] is a 1 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=5LMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LMC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d02|4d02]]</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=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5lmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmc OCA], [http://pdbe.org/5lmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmc RCSB], [http://www.ebi.ac.uk/pdbsum/5lmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmc ProSAT]</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=5lmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmc OCA], [https://pdbe.org/5lmc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lmc RCSB], [https://www.ebi.ac.uk/pdbsum/5lmc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NORV_ECOLI NORV_ECOLI]] Anaerobic nitric oxide reductase; uses NADH to detoxify nitric oxide (NO), protecting several 4Fe-4S NO-sensitive enzymes. Has at least 2 reductase partners, only one of which (NorW, flavorubredoxin reductase) has been identified. NO probably binds to the di-iron center; electrons enter from the reductase at rubredoxin and are transferred sequentially to the FMN center and the di-iron center. Also able to function as an aerobic oxygen reductase.<ref>PMID:11751865</ref> <ref>PMID:12101220</ref>
+[https://www.uniprot.org/uniprot/NORV_ECOLI NORV_ECOLI] Anaerobic nitric oxide reductase; uses NADH to detoxify nitric oxide (NO), protecting several 4Fe-4S NO-sensitive enzymes. Has at least 2 reductase partners, only one of which (NorW, flavorubredoxin reductase) has been identified. NO probably binds to the di-iron center; electrons enter from the reductase at rubredoxin and are transferred sequentially to the FMN center and the di-iron center. Also able to function as an aerobic oxygen reductase.<ref>PMID:11751865</ref> <ref>PMID:12101220</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Borges, P T]]
+[[Category: Escherichia coli K-12]]
-[[Category: Carrondo, M A]]
+[[Category: Large Structures]]
-[[Category: Frazao, C]]
+[[Category: Borges PT]]
-[[Category: Romao, C V]]
+[[Category: Carrondo MA]]
-[[Category: Teixeira, M]]
+[[Category: Frazao C]]
-[[Category: Vicente, J B]]
+[[Category: Romao CV]]
-[[Category: Diiron center]]
+[[Category: Teixeira M]]
-[[Category: Flavodiiron protein]]
+[[Category: Vicente JB]]
-[[Category: Flavorubredoxin]]
-[[Category: Nitric oxide reductase]]
-[[Category: Oxidoreductase]]

5lmc

From Proteopedia

Current revision

Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms from its rubredoxin domain

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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