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[[Image:1jk0.jpg|left|200px]]


{{Structure
==Ribonucleotide reductase Y2Y4 heterodimer==
|PDB= 1jk0 |SIZE=350|CAPTION= <scene name='initialview01'>1jk0</scene>, resolution 2.80&Aring;
<StructureSection load='1jk0' size='340' side='right'caption='[[1jk0]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>
<table><tr><td colspan='2'>[[1jk0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JK0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JK0 FirstGlance]. <br>
|ACTIVITY= [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]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
|GENE= RNR2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), RNR4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1jk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jk0 OCA], [https://pdbe.org/1jk0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jk0 RCSB], [https://www.ebi.ac.uk/pdbsum/1jk0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jk0 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RIR4_YEAST RIR4_YEAST] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR4 is required for proper folding of RNR2 and assembly with the large subunits.<ref>PMID:10535923</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jk/1jk0_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1jk0 ConSurf].
<div style="clear:both"></div>


'''Ribonucleotide reductase Y2Y4 heterodimer'''
==See Also==
 
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
 
== References ==
==Overview==
<references/>
The R2 subunits of class I ribonucleotide reductases (RNRs) house a diferric-tyrosyl radical (Y*) cofactor essential for DNA synthesis. In yeast, there are two R2 proteins, Y2 and Y4. Although both Y2 and Y4 are homologous to R2s from other organisms, Y4 lacks three conserved iron-binding residues, and its exact function is unclear. Y4 is required for assembly of the diferric-Y* cofactor in Y2, and the two proteins can form both homodimeric and heterodimeric complexes. The Y2Y4 heterodimer was crystallized from a mixture of the two proteins, and its structure was determined to 2.8 A resolution. Both Y2 and Y4 are completely alpha helical and resemble the mouse and Escherichia coli R2s in overall fold. Three alpha helices not observed in the mouse R2 structure are present at the Y2 N terminus, and one extra N-terminal helix is observed in Y4. In addition, one of the eight principal helices in both Y2 and Y4, alphaD, is shifted significantly from its position in mouse R2. The heterodimer interface is similar to the mouse R2 homodimer interface in size and interacting residues, but loop regions at the interface edges differ. A single metal ion, assigned as Zn(II), occupies the Fe2 position in the Y2 active site. Treatment of the crystals with Fe(II) results in difference electron density consistent with formation of a diiron center. No metal-binding site is observed in Y4. Instead, the residues in the active site region form a hydrogen-bonding network involving an arginine, two glutamic acids, and a water molecule.
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1JK0 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JK0 OCA].
 
==Reference==
Structure of the yeast ribonucleotide reductase Y2Y4 heterodimer., Voegtli WC, Ge J, Perlstein DL, Stubbe J, Rosenzweig AC, Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10073-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11526233 11526233]
[[Category: Protein complex]]
[[Category: Ribonucleoside-diphosphate reductase]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Ge, J.]]
[[Category: Ge J]]
[[Category: Perlstein, D L.]]
[[Category: Perlstein DL]]
[[Category: Rosenzweig, A C.]]
[[Category: Rosenzweig AC]]
[[Category: Stubbe, J.]]
[[Category: Stubbe J]]
[[Category: Voegtli, W C.]]
[[Category: Voegtli WC]]
[[Category: ZN]]
[[Category: r2]]
[[Category: ribonucleotide reductase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:04:27 2008''

Latest revision as of 10:40, 7 February 2024

Ribonucleotide reductase Y2Y4 heterodimerRibonucleotide reductase Y2Y4 heterodimer

Structural highlights

1jk0 is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIR4_YEAST Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR4 is required for proper folding of RNR2 and assembly with the large subunits.[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. ↑ Nguyen HH, Ge J, Perlstein DL, Stubbe J. Purification of ribonucleotide reductase subunits Y1, Y2, Y3, and Y4 from yeast: Y4 plays a key role in diiron cluster assembly. Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12339-44. PMID:10535923

1jk0, resolution 2.80Å

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