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4bmo

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Revision as of 07:18, 31 August 2022

Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex with NrdI (1.8 A resolution)

Structural highlights

4bmo is a 2 chain structure with sequence from Atcc 14579. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	4bmp
Activity:	Ribonucleoside-diphosphate reductase, with EC number 1.17.4.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[Q81G55_BACCR] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355] [B0YPL1_BACCE] Probably involved in ribonucleotide reductase function (By similarity).[SAAS:SAAS004465_004_003068]

Publication Abstract from PubMed

Class Ib ribonucleotide reductases (RNRs) use a dimetal-tyrosyl radical (Y*) cofactor in their NrdF (beta2) subunit to initiate ribonucleotide reduction in the NrdE (alpha2) subunit. Contrary to the diferric tyrosyl radical (Fe(III)2-Y*) cofactor, which can self-assemble from Fe(II)2-NrdF and O2, generation of the Mn(III)2-Y* cofactor requires the reduced form of a flavoprotein, NrdIhq, and O2 for its assembly. Here we report the 1.8 A resolution crystal structure of Bacillus cereus Fe2-NrdF in complex with NrdI. Compared to the previously solved Escherichia coli NrdI-Mn(II)2-NrdF structure, NrdI and NrdF binds similarly in Bacillus cereus through conserved core interactions. This protein-protein association seems to be unaffected by metal ion type bound in the NrdF subunit. The Bacillus cereus Mn(II)2-NrdF and Fe2-NrdF structures, also presented here, show conformational flexibility of residues surrounding the NrdF metal ion site. The movement of one of the metal-coordinating carboxylates is linked to the metal type present at the dimetal site and not associated with NrdI-NrdF binding. This carboxylate conformation seems to be vital for the water network connecting the NrdF dimetal site and the flavin in NrdI. From these observations, we suggest that metal-dependent variations in carboxylate coordination geometries are important for active Y* cofactor generation in class Ib RNRs. Additionally, we show that binding of NrdI to NrdF would structurally interfere with the suggested alpha2beta2 (NrdE-NrdF) holoenzyme formation, suggesting the potential requirement for NrdI dissociation before NrdE-NrdF assembly after NrdI-activation. The mode of interactions between the proteins involved in the class Ib RNR system is, however, not fully resolved.

Crystal Structure of Bacillus cereus Class Ib Ribonucleotide Reductase Di-iron NrdF in Complex with NrdI.,Hammerstad M, Hersleth HP, Tomter AB, Rohr AK, Andersson KK ACS Chem Biol. 2014 Feb 21;9(2):526-37. doi: 10.1021/cb400757h. Epub 2013 Dec 11. PMID:24295378^[1]

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

References

↑ Hammerstad M, Hersleth HP, Tomter AB, Rohr AK, Andersson KK. Crystal Structure of Bacillus cereus Class Ib Ribonucleotide Reductase Di-iron NrdF in Complex with NrdI. ACS Chem Biol. 2014 Feb 21;9(2):526-37. doi: 10.1021/cb400757h. Epub 2013 Dec 11. PMID:24295378 doi:http://dx.doi.org/10.1021/cb400757h

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/4bmo"

@@ Line 3: / Line 3: @@
 <StructureSection load='4bmo' size='340' side='right'caption='[[4bmo]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4bmo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BMO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BMO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4bmo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BMO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4bmp|4bmp]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4bmp|4bmp]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=4bmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bmo OCA], [http://pdbe.org/4bmo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bmo RCSB], [http://www.ebi.ac.uk/pdbsum/4bmo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bmo 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=4bmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bmo OCA], [https://pdbe.org/4bmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bmo RCSB], [https://www.ebi.ac.uk/pdbsum/4bmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bmo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q81G55_BACCR Q81G55_BACCR]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355] [[http://www.uniprot.org/uniprot/B0YPL1_BACCE B0YPL1_BACCE]] Probably involved in ribonucleotide reductase function (By similarity).[SAAS:SAAS004465_004_003068]
+[[https://www.uniprot.org/uniprot/Q81G55_BACCR Q81G55_BACCR]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355] [[https://www.uniprot.org/uniprot/B0YPL1_BACCE B0YPL1_BACCE]] Probably involved in ribonucleotide reductase function (By similarity).[SAAS:SAAS004465_004_003068]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 ==See Also==
-*[[Ribonucleotide reductase|Ribonucleotide reductase]]
+*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
 == References ==
 <references/>

4bmo

From Proteopedia

Revision as of 07:18, 31 August 2022

Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex with NrdI (1.8 A resolution)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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