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| | <StructureSection load='5r1r' size='340' side='right'caption='[[5r1r]], [[Resolution|resolution]] 3.10Å' scene=''> | | <StructureSection load='5r1r' size='340' side='right'caption='[[5r1r]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5r1r]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5R1R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5r1r]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5R1R FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NRDA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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]] 3.1Å</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>
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| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5r1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r1r OCA], [https://pdbe.org/5r1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5r1r RCSB], [https://www.ebi.ac.uk/pdbsum/5r1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5r1r 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=5r1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r1r OCA], [https://pdbe.org/5r1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5r1r RCSB], [https://www.ebi.ac.uk/pdbsum/5r1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5r1r ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r1/5r1r_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r1/5r1r_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ribonucleoside-diphosphate reductase]]
| + | [[Category: Eklund H]] |
| - | [[Category: Eklund, H]] | + | [[Category: Eriksson M]] |
| - | [[Category: Eriksson, M]] | + | |
| - | [[Category: Allosteric regulation]]
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| - | [[Category: Deoxyribonucleotide synthesis]]
| + | |
| - | [[Category: Radical chemistry]]
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| - | [[Category: Ribonucleotide reductase]]
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| - | [[Category: Specificity]]
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| Structural highlights
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
The invariant active site residue Glu441 in protein R1 of ribonucleotide reductase from Escherichia coli has been engineered to alanine, aspartic acid, and glutamic acid. Each mutant protein was structurally and enzymatically characterized. Glu441 contributes to substrate binding, and a carboxylate side chain at position 441 is essential for catalysis. The most intriguing results are the suicidal mechanism-based reaction intermediates observed when R1 E441Q is incubated with protein R2 and natural substrates (CDP and GDP). In a consecutive reaction sequence, we observe at least three clearly discernible steps: (i) a rapid decay (k1 >/= 1.2 s-1) of the catalytically essential tyrosyl radical of protein R2 concomitant with formation of an early transient radical intermediate species, (ii) a slower decay (k2 = 0.03 s-1) of the early intermediate concomitant with formation of another intermediate with a triplet EPR signal, and (iii) decay (k3 = 0.004 s-1) of the latter concomitant with formation of a characteristic substrate degradation product. The characteristics of the triplet EPR signal are compatible with a substrate radical intermediate (most likely localized at the 3'-position of the ribose moiety of the substrate nucleotide) postulated to occur in the wild type reaction mechanism as well.
A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase.,Persson AL, Eriksson M, Katterle B, Potsch S, Sahlin M, Sjoberg BM J Biol Chem. 1997 Dec 12;272(50):31533-41. PMID:9395490[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Persson AL, Eriksson M, Katterle B, Potsch S, Sahlin M, Sjoberg BM. A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase. J Biol Chem. 1997 Dec 12;272(50):31533-41. PMID:9395490
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