2xo4

From Proteopedia

(Difference between revisions)

Revision as of 10:35, 20 December 2023

RIBONUCLEOTIDE REDUCTASE Y730NH2Y MODIFIED R1 SUBUNIT OF E. COLI

Structural highlights

2xo4 is a 7 chain structure with sequence from Escherichia coli and 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 2.5Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIR1_ECOLI Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines.

Evolutionary Conservation

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

Publication Abstract from PubMed

Escherichia coli ribonucleotide reductase is an alpha2beta2 complex and catalyzes the conversion of nucleoside 5'-diphosphates (NDPs) to 2'-deoxynucleotides (dNDPs). The reaction is initiated by the transient oxidation of an active-site cysteine (C(439)) in alpha2 by a stable diferric tyrosyl radical (Y(122)*) cofactor in beta2. This oxidation occurs by a mechanism of long-range proton-coupled electron transfer (PCET) over 35 A through a specific pathway of residues: Y(122)*--> W(48)--> Y(356) in beta2 to Y(731)--> Y(730)--> C(439) in alpha2. To study the details of this process, 3-aminotyrosine (NH(2)Y) has been site-specifically incorporated in place of Y(356) of beta. The resulting protein, Y(356)NH(2)Y-beta2, and the previously generated proteins Y(731)NH(2)Y-alpha2 and Y(730)NH(2)Y-alpha2 (NH(2)Y-RNRs) are shown to catalyze dNDP production in the presence of the second subunit, substrate (S), and allosteric effector (E) with turnover numbers of 0.2-0.7 s(-1). Evidence acquired by three different methods indicates that the catalytic activity is inherent to NH(2)Y-RNRs and not the result of copurifying wt enzyme. The kinetics of formation of 3-aminotyrosyl radical (NH(2)Y*) at position 356, 731, and 730 have been measured with all S/E pairs. In all cases, NH(2)Y* formation is biphasic (k(fast) of 9-46 s(-1) and k(slow) of 1.5-5.0 s(-1)) and kinetically competent to be an intermediate in nucleotide reduction. The slow phase is proposed to report on the conformational gating of NH(2)Y* formation, while the k(cat) of approximately 0.5 s(-1) is proposed to be associated with rate-limiting oxidation by NH(2)Y* of the subsequent amino acid on the pathway during forward PCET. The X-ray crystal structures of Y(730)NH(2)Y-alpha2 and Y(731)NH(2)Y-alpha2 have been solved and indicate minimal structural changes relative to wt-alpha2. From the data, a kinetic model for PCET along the radical propagation pathway is proposed.

Kinetics of Radical Intermediate Formation and Deoxynucleotide Production in 3-Aminotyrosine-Substituted Escherichia coli Ribonucleotide Reductases.,Minnihan EC, Seyedsayamdost MR, Uhlin U, Stubbe J J Am Chem Soc. 2011 Jun 22;133(24):9430-40. Epub 2011 May 25. PMID:21612216^[1]

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

References

↑ Minnihan EC, Seyedsayamdost MR, Uhlin U, Stubbe J. Kinetics of Radical Intermediate Formation and Deoxynucleotide Production in 3-Aminotyrosine-Substituted Escherichia coli Ribonucleotide Reductases. J Am Chem Soc. 2011 Jun 22;133(24):9430-40. Epub 2011 May 25. PMID:21612216 doi:10.1021/ja201640n

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2xo4"

@@ Line 3: / Line 3: @@
 <StructureSection load='2xo4' size='340' side='right'caption='[[2xo4]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xo4]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XO4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XO4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xo4]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [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=2XO4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XO4 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TY2:3-AMINO-L-TYROSINE'>TY2</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]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rsr|1rsr]], [[1mxr|1mxr]], [[3r1r|3r1r]], [[1jqc|1jqc]], [[1pim|1pim]], [[2r1r|2r1r]], [[4r1r|4r1r]], [[2xav|2xav]], [[2xay|2xay]], [[2xap|2xap]], [[1piy|1piy]], [[2xak|2xak]], [[1biq|1biq]], [[1rlr|1rlr]], [[2xaw|2xaw]], [[1r65|1r65]], [[2alx|2alx]], [[1r1r|1r1r]], [[1av8|1av8]], [[7r1r|7r1r]], [[1xik|1xik]], [[1qfn|1qfn]], [[1mrr|1mrr]], [[2av8|2av8]], [[1rib|1rib]], [[1rnr|1rnr]], [[1jpr|1jpr]], [[5r1r|5r1r]], [[1pj1|1pj1]], [[1pfr|1pfr]], [[6r1r|6r1r]], [[1pj0|1pj0]], [[2xaz|2xaz]], [[2xax|2xax]], [[1rsv|1rsv]], [[1piu|1piu]], [[1yfd|1yfd]], [[2x0x|2x0x]], [[1piz|1piz]], [[1pm2|1pm2]], [[2xo5|2xo5]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TY2:3-AMINO-L-TYROSINE'>TY2</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=2xo4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xo4 OCA], [https://pdbe.org/2xo4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xo4 RCSB], [https://www.ebi.ac.uk/pdbsum/2xo4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xo4 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RIR1_ECOLI RIR1_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines. [[https://www.uniprot.org/uniprot/RIR2_ECOLI RIR2_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis.
+[https://www.uniprot.org/uniprot/RIR1_ECOLI RIR1_ECOLI] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Ribonucleoside-diphosphate reductase]]
+[[Category: Minnihan EC]]
-[[Category: Minnihan, E C]]
+[[Category: Seyedsayamdost MR]]
-[[Category: Seyedsayamdost, M R]]
+[[Category: Stubbe J]]
-[[Category: Stubbe, J]]
+[[Category: Uhlin U]]
-[[Category: Uhlin, U]]
-[[Category: Allosteric enzyme]]
-[[Category: Alternative initiation]]
-[[Category: Dna replication]]
-[[Category: Nucleotide-binding]]
-[[Category: Oxidoreductase]]

2xo4

From Proteopedia

Revision as of 10:35, 20 December 2023

RIBONUCLEOTIDE REDUCTASE Y730NH2Y MODIFIED R1 SUBUNIT OF E. COLI

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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