1ds7: Difference between revisions

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<StructureSection load='1ds7' size='340' side='right'caption='[[1ds7]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
<StructureSection load='1ds7' size='340' side='right'caption='[[1ds7]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ds7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_(strain_b) Escherichia coli (strain b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DS7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DS7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ds7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_B Escherichia coli B]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DS7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DS7 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2.06&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/6,7-dihydropteridine_reductase 6,7-dihydropteridine reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.34 1.5.1.34] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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=1ds7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ds7 OCA], [https://pdbe.org/1ds7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ds7 RCSB], [https://www.ebi.ac.uk/pdbsum/1ds7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ds7 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=1ds7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ds7 OCA], [https://pdbe.org/1ds7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ds7 RCSB], [https://www.ebi.ac.uk/pdbsum/1ds7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ds7 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/NFNB_ECOLI NFNB_ECOLI]] Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred. Capable of reducing nitrofurazone, quinones and the anti-tumor agent CB1954 (5-(aziridin-1-yl)-2,4-dinitrobenzamide). The reduction of CB1954 results in the generation of cytotoxic species.<ref>PMID:15684426</ref>
[https://www.uniprot.org/uniprot/NFSB_ECOLI NFSB_ECOLI] Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred. Capable of reducing nitrofurazone, quinones and the anti-tumor agent CB1954 (5-(aziridin-1-yl)-2,4-dinitrobenzamide). The reduction of CB1954 results in the generation of cytotoxic species.<ref>PMID:15684426</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1ds7 ConSurf].
</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=1ds7 ConSurf].
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== Publication Abstract from PubMed ==
The FMN-dependent flavoprotein nitroreductase from Escherichia coli B (NTR) is used in cancer chemotherapy to activate a range of prodrugs. The crystal structure of this enzyme has been determined, using molecular replacement methods and refined at 2.06 A resolution. The recombinant 24-kDa enzyme was crystallized in the tetragonal space group P4(1)2(1)2, with unit cell dimensions of a = b = 57.74 A and c = 275.51 A and two molecules in the asymmetric unit. The structure has a final R factor of 20.3% (R(free) = 26.7%), for all data between the resolution ranges of 10-2.06 A, and includes 4453 protein atoms, 230 water molecules, and 2 flavin mononucleotide (FMN) molecules. The functional unit is a homodimer, which forms the asymmetric unit in the crystal structure. The tertiary structures of these two monomers and their subunit interactions are nearly identical. The molecular replacement search model, the crystal structure of the major NAD(P)H:FMN oxidoreductase of Vibrio fisheri (FRase 1), was selected on the basis of its high sequence identity to that of NTR. The final superposition of these two enzymes revealed a very similar overall fold, with variation in the structures focused around surface loops and helices near the FMN cofactor. Helix G is implicated in substrate specificity and is better resolved in the present NTR structure than in the previously reported FRase 1 structure. The FMN binding pocket is also well-resolved, showing the presence of two channels leading into the active site. The amino acid side chains and main chain atoms interacting with the FMN are well-ordered. The structure of the substrate binding pocket has been used to examine substrate specificity and enzyme kinetics for prodrugs used in antibody-directed enzyme prodrug therapy (ADEPT) and gene-directed enzyme prodrug therapy (GDEPT).
Crystal structure of FMN-dependent nitroreductase from Escherichia coli B: a prodrug-activating enzyme.,Parkinson GN, Skelly JV, Neidle S J Med Chem. 2000 Oct 5;43(20):3624-31. PMID:11020276<ref>PMID:11020276</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ds7" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Nitroreductase|Nitroreductase]]
*[[Nitroreductase 3D structures|Nitroreductase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 6,7-dihydropteridine reductase]]
[[Category: Escherichia coli B]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Neidle, S]]
[[Category: Neidle S]]
[[Category: Parkinson, G]]
[[Category: Parkinson G]]
[[Category: Skelly, J]]
[[Category: Skelly J]]
[[Category: Flavoprotein]]
[[Category: Fmn]]
[[Category: Nitroreductase]]
[[Category: Oxidoreductase]]

Latest revision as of 09:58, 7 February 2024

A MINOR FMN-DEPENDENT NITROREDUCTASE FROM ESCHERICHIA COLI BA MINOR FMN-DEPENDENT NITROREDUCTASE FROM ESCHERICHIA COLI B

Structural highlights

1ds7 is a 2 chain structure with sequence from Escherichia coli B. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.06Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NFSB_ECOLI Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred. Capable of reducing nitrofurazone, quinones and the anti-tumor agent CB1954 (5-(aziridin-1-yl)-2,4-dinitrobenzamide). The reduction of CB1954 results in the generation of cytotoxic species.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Race PR, Lovering AL, Green RM, Ossor A, White SA, Searle PF, Wrighton CJ, Hyde EI. Structural and mechanistic studies of Escherichia coli nitroreductase with the antibiotic nitrofurazone. Reversed binding orientations in different redox states of the enzyme. J Biol Chem. 2005 Apr 8;280(14):13256-64. Epub 2005 Jan 31. PMID:15684426 doi:http://dx.doi.org/10.1074/jbc.M409652200

1ds7, resolution 2.06Å

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