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5j8d

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Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide

Structural highlights

5j8d is a 4 chain structure with sequence from Enterobacter cloacae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NFSB_ENTCL Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred.

Publication Abstract from PubMed

Nitroreductase (NR) from Enterobacter cloacae reduces diverse nitroaromatics including herbicides, explosives, and prodrugs, and holds promise for bioremediation, prodrug activation, and enzyme-assisted synthesis. We solved crystal structures of NR complexes with bound substrate or analog for each of its two half-reactions. We complemented these with kinetic isotope effect (KIE) measurements elucidating H-transfer steps essential to each half-reaction. KIEs indicate hydride transfer from NADH to the flavin consistent with our structure of NR with the NADH analog nicotinic acid adenine dinucleotide (NAAD). The KIE on reduction of p-nitrobenzoic acid (p-NBA) also indicates hydride transfer, and requires revision of prior computational mechanisms. Our mechanistic information provided a structural restraint for the orientation of bound substrate, placing the nitro group closer to the flavin N5 in the pocket that binds the amide of NADH. KIEs show that solvent provides a proton, enabling accommodation of different nitro group placements, consistent with the broad repertoire of NR.

Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase.,Pitsawong W, Haynes CA, Koder RL Jr, Rodgers DW, Miller AF Structure. 2017 Jul 5;25(7):978-987.e4. doi: 10.1016/j.str.2017.05.002. Epub 2017, Jun 1. PMID:28578873^[1]

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

References

↑ Pitsawong W, Haynes CA, Koder RL Jr, Rodgers DW, Miller AF. Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase. Structure. 2017 Jul 5;25(7):978-987.e4. doi: 10.1016/j.str.2017.05.002. Epub 2017, Jun 1. PMID:28578873 doi:http://dx.doi.org/10.1016/j.str.2017.05.002

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5j8d"

@@ Line 3: / Line 3: @@
 <StructureSection load='5j8d' size='340' side='right'caption='[[5j8d]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5j8d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J8D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5j8d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_cloacae Enterobacter cloacae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J8D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DND:NICOTINIC+ACID+ADENINE+DINUCLEOTIDE'>DND</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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]] 1.85&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kqb|1kqb]], [[1kqc|1kqc]], [[1kqd|1kqd]], [[5j8g|5j8g]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DND:NICOTINIC+ACID+ADENINE+DINUCLEOTIDE'>DND</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nfsB, nfnB, nfsI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</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=5j8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j8d OCA], [https://pdbe.org/5j8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j8d RCSB], [https://www.ebi.ac.uk/pdbsum/5j8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j8d ProSAT]</span></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=5j8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j8d OCA], [http://pdbe.org/5j8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j8d RCSB], [http://www.ebi.ac.uk/pdbsum/5j8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j8d ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NFSB_ENTCL NFSB_ENTCL]] Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred.
+[https://www.uniprot.org/uniprot/NFSB_ENTCL NFSB_ENTCL] Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 ==See Also==
-*[[Nitroreductase|Nitroreductase]]
+*[[Nitroreductase 3D structures|Nitroreductase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Enterobacter cloacae]]
 [[Category: Large Structures]]
-[[Category: Haynes, C A]]
+[[Category: Haynes CA]]
-[[Category: Koder, R L]]
+[[Category: Koder RL]]
-[[Category: Miller, A F]]
+[[Category: Miller AF]]
-[[Category: Rodgers, D W]]
+[[Category: Rodgers DW]]
-[[Category: Complex]]
-[[Category: Naad]]
-[[Category: Nitroreductase]]
-[[Category: Oxidoreductase]]
-[[Category: Substrate]]

5j8d

From Proteopedia

Current revision

Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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