2xay

From Proteopedia

(Difference between revisions)

Current revision

Ribonucleotide reductase Y730NO2Y and C439A modified R1 subunit of E. coli

Structural highlights

2xay is a 7 chain structure with sequence from Escherichia coli and Escherichia coli K-12. This structure supersedes the now removed PDB entry 2x3s. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.65Å
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

E. coli ribonucleotide reductase catalyzes the reduction of nucleoside 5'-diphosphates into 2'-deoxynucleotides and is composed of two subunits: alpha2 and beta2. During turnover, a stable tyrosyl radical (Y*) at Y(122)-beta2 reversibly oxidizes C(439) in the active site of alpha2. This radical propagation step is proposed to occur over 35 A, to use specific redox-active tyrosines (Y(122) and Y(356) in beta2, Y(731) and Y(730) in alpha2), and to involve proton-coupled electron transfer (PCET). 3-Nitrotyrosine (NO(2)Y, pK(a) 7.1) has been incorporated in place of Y(122), Y(731), and Y(730) to probe how the protein environment perturbs each pK(a) in the presence of the second subunit, substrate (S), and allosteric effector (E). The activity of each mutant is <4 x 10(-3) that of the wild-type (wt) subunit. The [NO(2)Y(730)]-alpha2 and [NO(2)Y(731)]-alpha2 each exhibit a pK(a) of 7.8-8.0 with E and E/beta2. The pK(a) of [NO(2)Y(730)]-alpha2 is elevated to 8.2-8.3 in the S/E/beta2 complex, whereas no further perturbation is observed for [NO(2)Y(731)]-alpha2. Mutations in pathway residues adjacent to the NO(2)Y that disrupt H-bonding minimally perturb its pK(a). The pK(a) of NO(2)Y(122)-beta2 alone or with alpha2/S/E is >9.6. X-ray crystal structures have been obtained for all [NO(2)Y]-alpha2 mutants (2.1-3.1 A resolution), which show minimal structural perturbation compared to wt-alpha2. Together with the pK(a) of the previously reported NO(2)Y(356)-beta2 (7.5 in the alpha2/S/E complex; Yee, C. et al. Biochemistry 2003, 42, 14541-14552), these studies provide a picture of the protein environment of the ground state at each Y in the PCET pathway, and are the starting point for understanding differences in PCET mechanisms at each residue in the pathway.

Site-Specific Incorporation of 3-Nitrotyrosine as a Probe of pK(a) Perturbation of Redox-Active Tyrosines in Ribonucleotide Reductase.,Yokoyama K, Uhlin U, Stubbe J J Am Chem Soc. 2010 Jun 2. PMID:20518462^[1]

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

References

↑ Yokoyama K, Uhlin U, Stubbe J. Site-Specific Incorporation of 3-Nitrotyrosine as a Probe of pK(a) Perturbation of Redox-Active Tyrosines in Ribonucleotide Reductase. J Am Chem Soc. 2010 Jun 2. PMID:20518462 doi:10.1021/ja101097p

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/2xay"

@@ Line 3: / Line 3: @@
 <StructureSection load='2xay' size='340' side='right'caption='[[2xay]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xay]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2x3s 2x3s]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XAY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xay]] 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]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2x3s 2x3s]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XAY FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NIY:META-NITRO-TYROSINE'>NIY</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]] 2.65&#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]], [[1pim|1pim]], [[1jqc|1jqc]], [[4r1r|4r1r]], [[2r1r|2r1r]], [[2xav|2xav]], [[2xap|2xap]], [[1piy|1piy]], [[2xak|2xak]], [[1biq|1biq]], [[1rlr|1rlr]], [[2xaw|2xaw]], [[2alx|2alx]], [[1r65|1r65]], [[1r1r|1r1r]], [[1av8|1av8]], [[7r1r|7r1r]], [[1xik|1xik]], [[2av8|2av8]], [[1mrr|1mrr]], [[1qfn|1qfn]], [[1rnr|1rnr]], [[1rib|1rib]], [[1jpr|1jpr]], [[5r1r|5r1r]], [[1pj1|1pj1]], [[1pfr|1pfr]], [[6r1r|6r1r]], [[1pj0|1pj0]], [[1rsv|1rsv]], [[1piu|1piu]], [[1yfd|1yfd]], [[1piz|1piz]], [[2x0x|2x0x]], [[1pm2|1pm2]], [[2xaz|2xaz]], [[2xax|2xax]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NIY:META-NITRO-TYROSINE'>NIY</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=2xay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xay OCA], [https://pdbe.org/2xay PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xay RCSB], [https://www.ebi.ac.uk/pdbsum/2xay PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xay 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: Stubbe J]]
-[[Category: Stubbe, J]]
+[[Category: Uhlin U]]
-[[Category: Uhlin, U]]
+[[Category: Yokoyama K]]
-[[Category: Yokoyama, K]]
-[[Category: Allosteric enzyme]]
-[[Category: Alternative initiation]]
-[[Category: Dna replication]]
-[[Category: Nucleotide-binding]]
-[[Category: Oxidoreductase]]

2xay

From Proteopedia

Current revision

Ribonucleotide reductase Y730NO2Y and C439A 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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