4d8f: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4d8f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydia_trachomatis Chlamydia trachomatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D8F FirstGlance]. <br>
<table><tr><td colspan='2'>[[4d8f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydia_trachomatis Chlamydia trachomatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D8F FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=4d8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8f OCA], [https://pdbe.org/4d8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d8f RCSB], [https://www.ebi.ac.uk/pdbsum/4d8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8f 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=4d8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8f OCA], [https://pdbe.org/4d8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d8f RCSB], [https://www.ebi.ac.uk/pdbsum/4d8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8f ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RIR2_CHLTR RIR2_CHLTR]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).
[https://www.uniprot.org/uniprot/RIR2_CHLTR RIR2_CHLTR] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The reaction of a class I ribonucleotide reductase (RNR) begins when a cofactor in the beta subunit oxidizes a cysteine residue approximately 35 A away in the alpha subunit, generating a thiyl radical. In the class Ic enzyme from Chlamydia trachomatis (Ct), the cysteine oxidant is the Mn(IV) ion of a Mn(IV)/Fe(III) cluster, which assembles in a reaction between O(2) and the Mn(II)/Fe(II) complex of beta. The heterodinuclear nature of the cofactor raises the question of which site, 1 or 2, contains the Mn(IV) ion. Because site 1 is closer to the conserved location of the cysteine-oxidizing tyrosyl radical of class Ia and Ib RNRs, we suggested that the Mn(IV) ion most likely resides in this site (i.e., (1)Mn(IV)/(2)Fe(III)), but a subsequent computational study favored its occupation of site 2 ((1)Fe(III)/(2)Mn(IV)). In this work, we have sought to resolve the location of the Mn(IV) ion in Ct RNR-beta by correlating X-ray crystallographic anomalous scattering intensities with catalytic activity for samples of the protein reconstituted in vitro by two different procedures. In samples containing primarily Mn(IV)/Fe(III) clusters, Mn preferentially occupies site 1, but some anomalous scattering from site 2 is observed, implying that both (1)Mn(II)/(2)Fe(II) and (1)Fe(II)/(2)Mn(II) complexes are competent to react with O(2) to produce the corresponding oxidized states. However, with diminished Mn(II) loading in the reconstitution, there is no evidence for Mn occupancy of site 2, and the greater activity of these "low-Mn" samples on a per-Mn basis implies that the (1)Mn(IV)/(2)Fe(III)-beta is at least the more active of the two oxidized forms and may be the only active form.
 
Evidence That the beta Subunit of Chlamydia trachomatis Ribonucleotide Reductase Is Active with the Manganese Ion of Its Manganese(IV)/Iron(III) Cofactor in Site 1.,Dassama LM, Boal AK, Krebs C, Rosenzweig AC, Bollinger JM J Am Chem Soc. 2012 Feb 8;134(5):2520-3. Epub 2012 Jan 25. PMID:22242660<ref>PMID:22242660</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4d8f" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
== References ==
<references/>
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__TOC__
</StructureSection>
</StructureSection>

Latest revision as of 17:28, 14 March 2024

Chlamydia trachomatis NrdB with a Mn/Fe cofactor (procedure 1 - high Mn)Chlamydia trachomatis NrdB with a Mn/Fe cofactor (procedure 1 - high Mn)

Structural highlights

4d8f is a 4 chain structure with sequence from Chlamydia trachomatis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIR2_CHLTR Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).

See Also

4d8f, resolution 2.20Å

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