Ribonucleotide reductase - Revision history

Michal Harel at 10:51, 17 January 2023

Michal Harel — Tue, 17 Jan 2023 10:51:59 GMT

←Older revision		Revision as of 10:51, 17 January 2023
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	For details on human RNR2 see [[P53R2]].<br />		For details on human RNR2 see [[P53R2]].<br />
	For mouse RNR see [[Mouse Ribonucleotide Reductase R2]].<br />		For mouse RNR see [[Mouse Ribonucleotide Reductase R2]].<br />
-	For RNR small subunit with nitrotyrosine modification see [[Nitrotyrosine]].	+	For RNR small subunit with nitrotyrosine modification see [[Nitrotyrosine]].<br />
		+	See also [[Ribonucleotide Reductase]].

	== Relevance ==		== Relevance ==

Michal Harel at 09:50, 16 December 2019

Michal Harel — Mon, 16 Dec 2019 09:50:01 GMT

←Older revision		Revision as of 09:50, 16 December 2019
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	</StructureSection>		</StructureSection>

-	== 3D Structures of Ribonucleotide reductase ==
-
-	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
-	{{#tree:id=OrganizedByTopic\|openlevels=0\|
-
-	*'''Class Ia ribonucleotide reductase'''
-
-	*Ribonucleotide reductase large subunit
-
-	**[[1zyz]], [[1zzd]], [[2cvs]], [[2cvt]], [[2cvu]], [[2cvv]], [[2cvw]], [[2cvx]], [[2cvy]] - yRNR R1 – yeast<BR />
-	**[[1rlr]] - EcRNR R1 – ''Escherichia coli''<br />
-	**[[1mrr]] - EcRNR R1 + Mn<br />
-	**[[5r1r]], [[6r1r]], [[7r1r]], [[1r1r]] – EcRNR R1 (mutant) + R2<br />
-
-	*''Ribonucleotide reductase large subunit complex''
-
-	**[[3hnc]] – hRNR M1 + TTP – human<BR />
-	**[[3hnd]] – hRNR M1 + GDP + TTP<BR />
-	**[[3hne]], [[3hnf]] – hRNR M1 + ATP + TTP<BR />
-	**[[2wgh]], [[5d1y]] - hRNR M1 + ATP + Mg<BR />
-	**[[6aui]] - hRNR M1 + ATP + CDP<br />
-	**[[5tus]], [[4x3v]] - hRNR M1 + inhibitor + TTP<br />
-	**[[3paw]] - yRNR R1 + ATP<BR />
-	**[[3k8t]] - yRNR R1 + ADP analog<BR />
-	**[[3s87]] - yRNR R1 + ADP + GTP<br />
-	**[[3s8a]] - yRNR R1 (mutant) + GTP<br />
-	**[[3tba]] - yRNR R1 (mutant) + GTP + ADP<br />
-	**[[3s8b]] - yRNR R1 + AMPPNP + CDP<br />
-	**[[3s8c]], [[3tb9]] - yRNR R1 (mutant) + AMPPNP + CDP<br />
-	**[[2zlf]], [[2zlg]] - yRNR R1 + peptide<BR />
-	**[[2eud]] - yRNR R1 + ligand<BR />
-	**[[3rsr]] – yRNR R1 + inhibitor<br />
-	**[[1qfn]] - EcRNR R1 + glutaredoxin 1<br />
-
-	*RNR small subunit
-
-	**[[3hf1]], [[2vux]], [[2uw2]], [[4djn]], [[3olj]] – hRNR M2<BR />
-	**[[3vpm]], [[3vpn]], [[3vpo]] – hRNR M2 (mutant)<br />
-	**[[1w68]], [[1h0n]], [[1h0o]], [[1xsm]] – mRNR R2 – mouse<BR />
-	**[[1smq]], [[1sms]] – yRNR 2<BR />
-	**[[1jk0]] – yRNR Y2+Y4<br />
-	**[[2xof]], [[1av8]], [[1rib]] – EcRNR R2 + Fe2O<BR />
-	**[[2alx]], [[1jqc]], [[1jpr]] - EcRNR R2 + Mn<br />
-	**[[1piy]], [[1r65]], [[1mxr]], [[1xik]] - EcRNR R2 + Fe<br />
-	**[[1piz]], [[1pj0]], [[1pj1]], [[1pim]], [[1piu]], [[1biq]], [[1pfr]] - EcRNR R2 (mutant) + Fe<BR />
-	**[[1yfd]], [[2av8]] - EcRNR R2 (mutant) + Fe2O<br />
-	**[[1pm2]] - EcRNR R2 (mutant) + Mn<br />
-	**[[2p1i]] – RNR R2 – ''Plasmodium yoelii''<BR />
-	**[[2o1z]] - RNR R2 – ''Plasmodium vivax''<BR />
-	**[[4d8f]], [[4d8g]], [[4m1i]] - CtRNR R2 + Fe + Mn<br />
-	**[[1syy]] - CtRNR R2 + Fe + Pb– ''Chlamydia trachomatis''<BR />
-	**[[2ani]] - CtRNR R2 (mutant) + Fe + Pb<BR />
-	**[[4m1h]] - CtRNR R2 <br />
-	**[[1uzr]] – MtRNR R2 – ''Mycobacterium tuberculosis''<BR />
-	**[[2rcc]] – RNR – ''Bacillus halodurans''<br />
-	**[[4n83]] - SsRNR + Mn<br />
-	**[[4hr5]] - GkRNR – ''Geobacillus kaustophilus''<br />
-	**[[5omj]], [[5omk]] - GkRNR + Fe <br />
-	**[[4hr0]], [[4hr4]] - GkRNR + Fe + Mn <br />
-	**[[6f6c]], [[6f6e]], [[6f6f]], [[6f6g]], [[6f6h]], [[6f6k]] - GkRNR (mutant) + Fe + Mn <br />
-	**[[6cwo]], [[6cwq]] - FjRNR + Mn – ''Flavobacterium johnsoniae''<br />
-
-	*''Ribonucleotide reductase small subunit complex''
-
-	**[[1w69]] – mRNR R2 + acetate<br />
-	**[[1rsr]], [[1rsv]] - EcRNR R2 (mutant) + Fe + N3<BR />
-	**[[1rnr]] – EcRNR R2 (mutant) + Fe + dopa<BR />
-	**[[5ci4]] – EcRNR R2 (mutant) + Fe2O<br />
-	**[[5ci3]], [[5ci0]], [[5ci1]], [[5ci2]] – EcRNR R2 (mutant) + fluoro-tyrosine + Fe<sub>2</sub>O<br />
-	**[[6cwp]] – FjRNR + Mn + peptide<br />
-	**[[4xbw]] – GkRNR + Mn<br />
-	**[[6i94]] – GkRNR (mutant) + Mn<br />
-	**[[5dco]], [[4xb9]], [[4xbv]] – GkRNR + Fe<br />
-	**[[6i93]] – GkRNR (mutant) + Fe<br />
-	**[5dcr]], [[5dcs]] – GkRNR + Mn + Fe<br />
-	**[[6i90]], [[6i92]], [[6i95]], [[6f6b]], [[6f6l]], [[6f6m]], [[5ekb]] – GkRNR (mutant) + Mn + Fe<br />
-	**[[4ac8]] – MtRNR + Mn + Fe<br />
-
-	*Ribonucleotide reductase small+large subunit
-
-	**[[3uus]] - EcRNR R1+ R2 + Fe + ATP<br />
-	**[[4erm]] - EcRNR R1+ R2 + Fe2O + ATP + ADP<br />
-	**[[4erp]] - EcRNR R1+ R2 + Fe2O + ATP<br />
-	**[[2xak]], [[2xap]], [[2xo4]], [[2xo5]] - EcRNR R1 modified+ R2 peptide<BR />
-	**[[2xav]], [[2xaw]], [[2xax]], [[2xay]], [[2xaz]], [[2x0x]] - EcRNR R1 (mutant) modified + R2 peptide<BR />
-	**[[5cns]], [[5cnt]], [[5cnv]], [[5cnu]] - EcRNR R1 + R2 + Fe2O + 2 nucleotides<br />
-	**[[2r1r]] - EcRNR R1 + R2 + TTP<BR />
-	**[[3r1r]] - EcRNR R1 + R2 + AMPPNP<BR />
-	**[[4r1r]] - EcRNR R1 + R2 + GDP + TTP<BR />
-	**[[2bq1]] - StRNR R1+ R2<br />
-	**[[5im3]] - RNR + dATP – ''Pseudomonas aeruginosa''<br />
-
-	*'''Class Ib RNR''' ; NrdE – large subunit; NrdF – small subunit
-
-	**[[6cgm]] - BaRNR NrdE – ''Bacillus subtilis''<br />
-	**[[4dr0]] - BaRNR NrdF + Mn <br />
-	**[[6myx]] - BaRNR NrdE + DTP – Cryo EM<br />
-	**[[6mv9]] - BaRNR NrdE + TTP + ADP <br />
-	**[[6mt9]], [[6mve]] - BaRNR NrdE + TTP + ADP + ATP <br />
-	**[[6mw3]] - BaRNR NrdE + NrdF + DTP – Cryo EM<br />
-	**[[6cgn]], [[6cgl]] - BaRNR NrdE + AMP derivative <br />
-	**[[1pem]] - StRNR NrdE – Salmonella typhimurium<br />
-	**[[1peo]], [[1peq]], [[1peu]] - StRNR NrdE + nucleotide<br />
-	**[[2bq1]] - StRNR NrdE + NrdF + Fe + GTP<br />
-	**[[1r2f]] - StRNR NrdF + Fe<br />
-	**[[2r2f]] - StRNR NrdF + Fe2O<br />
-	**[[4dr0]] - BaRNR NrdF + Mn <br />
-	**[[4bmq]], [[4bmr]], [[4bmt]] - BcRNR NrdF + Fe – ''Bacillus cereus''<br />
-	**[[4bmu]] - BcRNR NrdF + Mn<br />
-	**[[4bmo]], [[4bmp]] - BcRNR NrdF + NrdI + Fe + FMN<br />
-	**[[4m1f]] - EcRNR NrdF<br />
-	**[[3n37]] - EcRNR NrdF + Mn<br />
-	**[[3n38]] - EcRNR NrdF + Fe<br />
-	**[[3n39]], [[3n3a]] - EcRNR NrdF + NrdI + Mn + FMN<br />
-	**[[3n3b]] - EcRNR NrdF + NrdI + Mn + FMN + Fe2O<br />
-	**[[4n82]] – SsRNR + FMN – ''Streptococcus sanguinis''<br />
-	**[[4n83]] - SsRNR NrdF + Mn<br />
-	**[[3mjo]] - CaRNR NrdF + Mn - ''Corynebacterium ammoniagenes'' <br />
-	**[[1kgn]], [[1kgo]], [[1kgp]], [[1oqu]], [[3dhz]] - CaRNR NrdF + Fe<br />
-
-	*'''Class II ribonucleotide reductase'''
-
-	**[[1xjf]], [[4col]] – TmRNR + DATP – ''Thermotoga maritima''<BR />
-	**[[4coi]], [[4com]], [[4con]] – TmRNR<br />
-	**[[1xjg]], [[1xjk]], [[1xje]], [[1xjn]], [[4coj]] - TmRNR + 2 nucleotides<BR />
-	**[[1xjj]] - TmRNR + GTP<BR />
-	**[[1xjm]] - TmRNR + TTP<BR />
-	**[[3o0n]] - TmRNR + TTP + Co + Mg + deoxyadenosine + B12<br />
-	**[[3o0o]] - TmRNR + TTP + GDP + Mg + deoxyadenosine + B12<br />
-	**[[3o0q]] - TmRNR + TTP + GDP + Mg + adenosine <br />
-	**[[1l1l]] – RNR (mutant) – ''Lactobacillus leichmannii''<br />
-
-	*'''Class III ribonucleotide reductase'''
-
-	**[[1h78]], [[1h79]], [[1h7a]], [[1hk8]] – T4RNR (mutant) + nucleotide triphosphate – bacteriophage T4<br />
-	**[[1h7b]] – T4RNR (mutant) <br />
-	**[[4u3e]] – TmRNR large subunit <br />
-	}}
	== References ==		== References ==
	<references/>		<references/>
-
-
-
-
-

	[[Category:Topic Page]]		[[Category:Topic Page]]

Michal Harel at 09:48, 16 December 2019

Michal Harel — Mon, 16 Dec 2019 09:48:53 GMT

←Older revision		Revision as of 09:48, 16 December 2019
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	== 3D Structures of Ribonucleotide reductase ==		== 3D Structures of Ribonucleotide reductase ==
-	[[Ribonucleotide reductase ==	+	[[Ribonucleotide reductase 3D structures]]

	</StructureSection>		</StructureSection>

Michal Harel at 09:48, 16 December 2019

Michal Harel — Mon, 16 Dec 2019 09:48:19 GMT

←Older revision		Revision as of 09:48, 16 December 2019
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	*<scene name='46/461381/Cv/6'>dATP binding site</scene>. Water molecules are shown as red spheres.		*<scene name='46/461381/Cv/6'>dATP binding site</scene>. Water molecules are shown as red spheres.
	*<scene name='46/461381/Cv/7'>UDP binding site</scene>.		*<scene name='46/461381/Cv/7'>UDP binding site</scene>.
		+
		+	== 3D Structures of Ribonucleotide reductase ==
		+	[[Ribonucleotide reductase ==
		+
	</StructureSection>		</StructureSection>

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	**[[1zyz]], [[1zzd]], [[2cvs]], [[2cvt]], [[2cvu]], [[2cvv]], [[2cvw]], [[2cvx]], [[2cvy]] - yRNR R1 – yeast<BR />		**[[1zyz]], [[1zzd]], [[2cvs]], [[2cvt]], [[2cvu]], [[2cvv]], [[2cvw]], [[2cvx]], [[2cvy]] - yRNR R1 – yeast<BR />
-	**[[~~1r1r~~]] - EcRNR R1 – ''Escherichia coli''<br />	+	**[[1rlr]] - EcRNR R1 – ''Escherichia coli''<br />
	**[[1mrr]] - EcRNR R1 + Mn<br />		**[[1mrr]] - EcRNR R1 + Mn<br />
	**[[5r1r]], [[6r1r]], [[7r1r]], [[1r1r]] – EcRNR R1 (mutant) + R2<br />		**[[5r1r]], [[6r1r]], [[7r1r]], [[1r1r]] – EcRNR R1 (mutant) + R2<br />
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	*RNR small subunit		*RNR small subunit

		+	**[[3hf1]], [[2vux]], [[2uw2]], [[4djn]], [[3olj]] – hRNR M2<BR />
		+	**[[3vpm]], [[3vpn]], [[3vpo]] – hRNR M2 (mutant)<br />
		+	**[[1w68]], [[1h0n]], [[1h0o]], [[1xsm]] – mRNR R2 – mouse<BR />
		+	**[[1smq]], [[1sms]] – yRNR 2<BR />
		+	**[[1jk0]] – yRNR Y2+Y4<br />
	**[[2xof]], [[1av8]], [[1rib]] – EcRNR R2 + Fe2O<BR />		**[[2xof]], [[1av8]], [[1rib]] – EcRNR R2 + Fe2O<BR />
	**[[2alx]], [[1jqc]], [[1jpr]] - EcRNR R2 + Mn<br />		**[[2alx]], [[1jqc]], [[1jpr]] - EcRNR R2 + Mn<br />
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	**[[1yfd]], [[2av8]] - EcRNR R2 (mutant) + Fe2O<br />		**[[1yfd]], [[2av8]] - EcRNR R2 (mutant) + Fe2O<br />
	**[[1pm2]] - EcRNR R2 (mutant) + Mn<br />		**[[1pm2]] - EcRNR R2 (mutant) + Mn<br />
-	**[[3hf1]], [[2vux]], [[2uw2]], [[4djn]] – hRNR M2<BR />
	**[[2p1i]] – RNR R2 – ''Plasmodium yoelii''<BR />		**[[2p1i]] – RNR R2 – ''Plasmodium yoelii''<BR />
	**[[2o1z]] - RNR R2 – ''Plasmodium vivax''<BR />		**[[2o1z]] - RNR R2 – ''Plasmodium vivax''<BR />
-	**[[1w68]], [[1h0n]], [[1h0o]], [[1xsm]] – mRNR R2 – mouse<BR />
-	**[[1smq]], [[1sms]] – yRNR 2<BR />
	**[[4d8f]], [[4d8g]], [[4m1i]] - CtRNR R2 + Fe + Mn<br />		**[[4d8f]], [[4d8g]], [[4m1i]] - CtRNR R2 + Fe + Mn<br />
	**[[1syy]] - CtRNR R2 + Fe + Pb– ''Chlamydia trachomatis''<BR />		**[[1syy]] - CtRNR R2 + Fe + Pb– ''Chlamydia trachomatis''<BR />
	**[[2ani]] - CtRNR R2 (mutant) + Fe + Pb<BR />		**[[2ani]] - CtRNR R2 (mutant) + Fe + Pb<BR />
	**[[4m1h]] - CtRNR R2 <br />		**[[4m1h]] - CtRNR R2 <br />
-	**[[1uzr]] – ~~RNR~~ R2 – ''Mycobacterium tuberculosis''<BR />	+	**[[1uzr]] – MtRNR R2 – ''Mycobacterium tuberculosis''<BR />
-	**[[3olj]] – hRNR M2<br />	+
-	**[[1jk0]] – yRNR Y2+Y4<br />	+
-	**[[3vpm]], [[3vpn]], [[3vpo]] – hRNR M2 (mutant)<br />	+
	**[[2rcc]] – RNR – ''Bacillus halodurans''<br />		**[[2rcc]] – RNR – ''Bacillus halodurans''<br />
	**[[4n83]] - SsRNR + Mn<br />		**[[4n83]] - SsRNR + Mn<br />
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	*''Ribonucleotide reductase small subunit complex''		*''Ribonucleotide reductase small subunit complex''

		+	**[[1w69]] – mRNR R2 + acetate<br />
	**[[1rsr]], [[1rsv]] - EcRNR R2 (mutant) + Fe + N3<BR />		**[[1rsr]], [[1rsv]] - EcRNR R2 (mutant) + Fe + N3<BR />
	**[[1rnr]] – EcRNR R2 (mutant) + Fe + dopa<BR />		**[[1rnr]] – EcRNR R2 (mutant) + Fe + dopa<BR />
	**[[5ci4]] – EcRNR R2 (mutant) + Fe2O<br />		**[[5ci4]] – EcRNR R2 (mutant) + Fe2O<br />
	**[[5ci3]], [[5ci0]], [[5ci1]], [[5ci2]] – EcRNR R2 (mutant) + fluoro-tyrosine + Fe<sub>2</sub>O<br />		**[[5ci3]], [[5ci0]], [[5ci1]], [[5ci2]] – EcRNR R2 (mutant) + fluoro-tyrosine + Fe<sub>2</sub>O<br />
-	**[[1w69]] – mRNR R2 + acetate<br />
	**[[6cwp]] – FjRNR + Mn + peptide<br />		**[[6cwp]] – FjRNR + Mn + peptide<br />
		+	**[[4xbw]] – GkRNR + Mn<br />
		+	**[[6i94]] – GkRNR (mutant) + Mn<br />
		+	**[[5dco]], [[4xb9]], [[4xbv]] – GkRNR + Fe<br />
		+	**[[6i93]] – GkRNR (mutant) + Fe<br />
		+	**[5dcr]], [[5dcs]] – GkRNR + Mn + Fe<br />
		+	**[[6i90]], [[6i92]], [[6i95]], [[6f6b]], [[6f6l]], [[6f6m]], [[5ekb]] – GkRNR (mutant) + Mn + Fe<br />
		+	**[[4ac8]] – MtRNR + Mn + Fe<br />

	*Ribonucleotide reductase small+large subunit		*Ribonucleotide reductase small+large subunit
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	**[[5im3]] - RNR + dATP – ''Pseudomonas aeruginosa''<br />		**[[5im3]] - RNR + dATP – ''Pseudomonas aeruginosa''<br />

-	*'''Class Ib RNR'''	+	*'''Class Ib RNR''' ; NrdE – large subunit; NrdF – small subunit

-	**[[6cgm]] - BaRNR ~~subunit~~ NrdE – ''Bacillus subtilis''<br />	+	**[[6cgm]] - BaRNR NrdE – ''Bacillus subtilis''<br />
-	**[[6cgn]], [[6cgl]] - BaRNR ~~subunit~~ NrdE + AMP derivative <br />	+	**[[4dr0]] - BaRNR NrdF + Mn <br />
		+	**[[6myx]] - BaRNR NrdE + DTP – Cryo EM<br />
		+	**[[6mv9]] - BaRNR NrdE + TTP + ADP <br />
		+	**[[6mt9]], [[6mve]] - BaRNR NrdE + TTP + ADP + ATP <br />
		+	**[[6mw3]] - BaRNR NrdE + NrdF + DTP – Cryo EM<br />
		+	**[[6cgn]], [[6cgl]] - BaRNR NrdE + AMP derivative <br />
	**[[1pem]] - StRNR NrdE – Salmonella typhimurium<br />		**[[1pem]] - StRNR NrdE – Salmonella typhimurium<br />
	**[[1peo]], [[1peq]], [[1peu]] - StRNR NrdE + nucleotide<br />		**[[1peo]], [[1peq]], [[1peu]] - StRNR NrdE + nucleotide<br />
	**[[2bq1]] - StRNR NrdE + NrdF + Fe + GTP<br />		**[[2bq1]] - StRNR NrdE + NrdF + Fe + GTP<br />
-	**[[4dr0]] - BaRNR ~~subunit~~ NrdF + Mn <br />	+	**[[1r2f]] - StRNR NrdF + Fe<br />
		+	**[[2r2f]] - StRNR NrdF + Fe2O<br />
		+	**[[4dr0]] - BaRNR NrdF + Mn <br />
	**[[4bmq]], [[4bmr]], [[4bmt]] - BcRNR NrdF + Fe – ''Bacillus cereus''<br />		**[[4bmq]], [[4bmr]], [[4bmt]] - BcRNR NrdF + Fe – ''Bacillus cereus''<br />
	**[[4bmu]] - BcRNR NrdF + Mn<br />		**[[4bmu]] - BcRNR NrdF + Mn<br />
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	**[[4n82]] – SsRNR + FMN – ''Streptococcus sanguinis''<br />		**[[4n82]] – SsRNR + FMN – ''Streptococcus sanguinis''<br />
	**[[4n83]] - SsRNR NrdF + Mn<br />		**[[4n83]] - SsRNR NrdF + Mn<br />
-	**[[1r2f]] - StRNR NrdF + Fe<br />	+	**[[3mjo]] - CaRNR NrdF + Mn - ''Corynebacterium ammoniagenes'' <br />
-	**[[2r2f]] - StRNR NrdF + Fe2O<br />	+	**[[1kgn]], [[1kgo]], [[1kgp]], [[1oqu]], [[3dhz]] - CaRNR NrdF + Fe<br />
-	**[[3mjo]] - ~~CcRNR~~ NrdF + Mn - ''Corynebacterium ammoniagenes'' <br />	+
-	**[[1kgn]], [[1kgo]], [[1kgp]], [[1oqu]], [[3dhz]] - ~~CcRNR~~ NrdF + Fe<br />	+

	*'''Class II ribonucleotide reductase'''		*'''Class II ribonucleotide reductase'''

Alexander Berchansky at 13:26, 27 August 2019

Alexander Berchansky — Tue, 27 Aug 2019 13:26:49 GMT

←Older revision		Revision as of 13:26, 27 August 2019
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	== Structural highlights ==		== Structural highlights ==
-	Class II RNR is <scene name='46/461381/Cv/2'>vitamin B12-dependent</scene>. The active site which binds the substrate is in a tight pocket and contains conserved residues involved in the catalytic mechanism <ref>PMID:15475969</ref>.	+	Class II RNR is <scene name='46/461381/Cv/5'>vitamin B12-dependent</scene>. The active site which binds the substrate is in a tight pocket and contains conserved residues involved in the catalytic mechanism <ref>PMID:15475969</ref>.
-	*<scene name='46/461381/Cv/3'>dATP binding site</scene>.	+	*<scene name='46/461381/Cv/6'>dATP binding site</scene>. Water molecules are shown as red spheres.
-	*<scene name='46/461381/Cv/4'>UDP binding site</scene>.	+	*<scene name='46/461381/Cv/7'>UDP binding site</scene>.
	</StructureSection>		</StructureSection>

Michal Harel at 08:57, 16 October 2018

Michal Harel — Tue, 16 Oct 2018 08:57:34 GMT

←Older revision		Revision as of 08:57, 16 October 2018
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	* '''Class Ia RNR''' is a tetramer composed from large (RNR1) and small (RNR2) subunits. Class I RNR is iron-dependent and produces tyrosyl radical. Thimidine triphosphate (TTP) is an effector in the reaction<ref>PMID:21456967</ref>.<br />		* '''Class Ia RNR''' is a tetramer composed from large (RNR1) and small (RNR2) subunits. Class I RNR is iron-dependent and produces tyrosyl radical. Thimidine triphosphate (TTP) is an effector in the reaction<ref>PMID:21456967</ref>.<br />
	* ''' Class Ib RNR''' contains 2 proteins: α (NrdE) and β (NrdF)<ref>PMID:21250660</ref>.<br />		* ''' Class Ib RNR''' contains 2 proteins: α (NrdE) and β (NrdF)<ref>PMID:21250660</ref>.<br />
-	''E. Coli'' contains two types of RNR: the aerobic RNR belongs to class Ia and is composed of proteins R1 and R2, the anaerobic RNR belongs to class Ib. <br />	+	''E. Coli'' contains two types of RNR: the aerobic RNR belongs to class Ia and is composed of proteins R1 and R2, the anaerobic RNR belongs to class Ib<ref>PMID:17496099</ref>. <br />
	* ''' Class II RNR''' reduces ribonucleotide triphosphates using coenzyme B12<ref>PMID:11875520</ref>.<br />		* ''' Class II RNR''' reduces ribonucleotide triphosphates using coenzyme B12<ref>PMID:11875520</ref>.<br />
	* '''Class III RNR''' generate glycine radical using S-adenosyl methionine and Fe-S center<ref>PMID:17606358</ref>.<br />		* '''Class III RNR''' generate glycine radical using S-adenosyl methionine and Fe-S center<ref>PMID:17606358</ref>.<br />

Michal Harel at 08:50, 16 October 2018

Michal Harel — Tue, 16 Oct 2018 08:50:52 GMT

←Older revision		Revision as of 08:50, 16 October 2018
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	**[[5im3]] - RNR + dATP – ''Pseudomonas aeruginosa''<br />		**[[5im3]] - RNR + dATP – ''Pseudomonas aeruginosa''<br />

-	Class Ib RNR	+	*'''Class Ib RNR'''

	**[[6cgm]] - BaRNR subunit NrdE – ''Bacillus subtilis''<br />		**[[6cgm]] - BaRNR subunit NrdE – ''Bacillus subtilis''<br />

Michal Harel at 08:50, 16 October 2018

Michal Harel — Tue, 16 Oct 2018 08:50:00 GMT

←Older revision		Revision as of 08:50, 16 October 2018
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	{{#tree:id=OrganizedByTopic\|openlevels=0\|		{{#tree:id=OrganizedByTopic\|openlevels=0\|

-	*'''Class I ribonucleotide reductase'''	+	*'''Class Ia ribonucleotide reductase'''

	*Ribonucleotide reductase large subunit		*Ribonucleotide reductase large subunit

Michal Harel at 08:39, 16 October 2018

Michal Harel — Tue, 16 Oct 2018 08:39:23 GMT

←Older revision		Revision as of 08:39, 16 October 2018
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	== Function ==		== Function ==
	'''Ribonucleotide reductase''' (RNR) or '''ribonucleotide-diphosphate reductase''' catalyzes the formation of deoxyribonucleotides from ribonucleotides<ref>PMID:16756507</ref>. There are 3 classes of RNR.<br />		'''Ribonucleotide reductase''' (RNR) or '''ribonucleotide-diphosphate reductase''' catalyzes the formation of deoxyribonucleotides from ribonucleotides<ref>PMID:16756507</ref>. There are 3 classes of RNR.<br />
-	* '''Class I RNR''' is a tetramer composed from large (RNR1) and small (RNR2) subunits. Class I RNR is iron-dependent and produces tyrosyl radical. Thimidine triphosphate (TTP) is an effector in the reaction<ref>PMID:21456967</ref>.<br />	+	* '''Class Ia RNR''' is a tetramer composed from large (RNR1) and small (RNR2) subunits. Class I RNR is iron-dependent and produces tyrosyl radical. Thimidine triphosphate (TTP) is an effector in the reaction<ref>PMID:21456967</ref>.<br />
	* ''' Class Ib RNR''' contains 2 proteins: α (NrdE) and β (NrdF)<ref>PMID:21250660</ref>.<br />		* ''' Class Ib RNR''' contains 2 proteins: α (NrdE) and β (NrdF)<ref>PMID:21250660</ref>.<br />
		+	''E. Coli'' contains two types of RNR: the aerobic RNR belongs to class Ia and is composed of proteins R1 and R2, the anaerobic RNR belongs to class Ib. <br />
	* ''' Class II RNR''' reduces ribonucleotide triphosphates using coenzyme B12<ref>PMID:11875520</ref>.<br />		* ''' Class II RNR''' reduces ribonucleotide triphosphates using coenzyme B12<ref>PMID:11875520</ref>.<br />
	* '''Class III RNR''' generate glycine radical using S-adenosyl methionine and Fe-S center<ref>PMID:17606358</ref>.<br />		* '''Class III RNR''' generate glycine radical using S-adenosyl methionine and Fe-S center<ref>PMID:17606358</ref>.<br />
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	**[[1zyz]], [[1zzd]], [[2cvs]], [[2cvt]], [[2cvu]], [[2cvv]], [[2cvw]], [[2cvx]], [[2cvy]] - yRNR R1 – yeast<BR />		**[[1zyz]], [[1zzd]], [[2cvs]], [[2cvt]], [[2cvu]], [[2cvv]], [[2cvw]], [[2cvx]], [[2cvy]] - yRNR R1 – yeast<BR />
-	**[[1r1r~~]], [[1rlr]], [[1mrr~~]] - EcRNR R1 – ''Escherichia coli''<br />	+	**[[1r1r]] - EcRNR R1 – ''Escherichia coli''<br />
-	**[[5r1r]], [[6r1r]], [[7r1r]] - EcRNR R1 (mutant)~~<br />~~	+	**[[1mrr]] - EcRNR R1 + Mn<br />
-	**[[4n82]] – SsRNR – ''Streptococcus sanguinis''<br />	+	**[[5r1r]], [[6r1r]], [[7r1r]], [[1r1r]] – EcRNR R1 (mutant) + R2<br />

	*''Ribonucleotide reductase large subunit complex''		*''Ribonucleotide reductase large subunit complex''
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	**[[2zlf]], [[2zlg]] - yRNR R1 + peptide<BR />		**[[2zlf]], [[2zlg]] - yRNR R1 + peptide<BR />
	**[[2eud]] - yRNR R1 + ligand<BR />		**[[2eud]] - yRNR R1 + ligand<BR />
-	**[[3rsr]] – yRNR + inhibitor<br />	+	**[[3rsr]] – yRNR R1 + inhibitor<br />
-	**[[2r1r]] - EcRNR R1 + TTP<BR />	+
-	**[[3r1r]] - EcRNR R1 + AMPPNP<BR />	+
-	**[[4r1r]] - EcRNR R1 + GDP + TTP<BR />	+
	**[[1qfn]] - EcRNR R1 + glutaredoxin 1<br />		**[[1qfn]] - EcRNR R1 + glutaredoxin 1<br />
-	**[[1peu]] - StRNR + DTP - ''Salmonella typhimurium''<br />

	*RNR small subunit		*RNR small subunit

-	**[[2xof]], [[~~3n37~~]], [[~~3n38~~]], [[2alx~~]], [[1piy]], [[1r65]], [[1mxr~~]], [[1jqc]], [[1jpr]], [[~~1av8~~]], [[~~1xik~~]], [[~~1rib~~]], [[~~4m1f~~]]~~, [[5ci4]], [[4xbw]], [[5dco]], [[5dcr]], [[5dcs]], [[5ekb]], [[4xb9]], [[4xbv]] –~~ EcRNR R2 <BR />	+	**[[2xof]], [[1av8]], [[1rib]] – EcRNR R2 + Fe2O<BR />
-	**~~[[1yfd]],~~ [[1piz]], [[1pj0]], [[1pj1~~]], [[1pm2~~]], [[1pim]], [[1piu]], [[1biq~~]], [[2av8~~]], [[1pfr]], [[~~5ci0~~]], [[~~5ci1~~]], [[~~5ci2]], [[5ci3~~]] - EcRNR R2 (mutant) + Fe<BR />	+	**[[2alx]], [[1jqc]], [[1jpr]] - EcRNR R2 + Mn<br />
		+	**[[1piy]], [[1r65]], [[1mxr]], [[1xik]] - EcRNR R2 + Fe<br />
		+	**[[1piz]], [[1pj0]], [[1pj1]], [[1pim]], [[1piu]], [[1biq]], [[1pfr]] - EcRNR R2 (mutant) + Fe<BR />
		+	**[[1yfd]], [[2av8]] - EcRNR R2 (mutant) + Fe2O<br />
		+	**[[1pm2]] - EcRNR R2 (mutant) + Mn<br />
	**[[3hf1]], [[2vux]], [[2uw2]], [[4djn]] – hRNR M2<BR />		**[[3hf1]], [[2vux]], [[2uw2]], [[4djn]] – hRNR M2<BR />
-	**[[3mjo]], [[3dhz]], [[1oqu]], [[1kgn]], [[1kgo]], [[1kgp]] – RNR R2 – ''Corynebacterium ammoniagenes''<BR />
	**[[2p1i]] – RNR R2 – ''Plasmodium yoelii''<BR />		**[[2p1i]] – RNR R2 – ''Plasmodium yoelii''<BR />
	**[[2o1z]] - RNR R2 – ''Plasmodium vivax''<BR />		**[[2o1z]] - RNR R2 – ''Plasmodium vivax''<BR />
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	*''Ribonucleotide reductase small subunit complex''		*''Ribonucleotide reductase small subunit complex''

-	**[[1rsr]], [[1rsv]] - EcRNR R2 (mutant) + N3~~<BR />~~	+	**[[1rsr]], [[1rsv]] - EcRNR R2 (mutant) + Fe + N3<BR />
-	**[[3n39]], [[3n3a]], [[3n3b]] – EcRNR R2 + NrdI<BR />	+	**[[1rnr]] – EcRNR R2 (mutant) + Fe + dopa<BR />
-	**[[1rnr]] – EcRNR R2 (mutant) + dopa<BR />	+	**[[5ci4]] – EcRNR R2 (mutant) + Fe2O<br />
-	**[[5ci4]] – EcRNR R2 (mutant) + ~~FE2O~~<br />	+	**[[5ci3]], [[5ci0]], [[5ci1]], [[5ci2]] – EcRNR R2 (mutant) + fluoro-tyrosine + Fe<sub>2</sub>O<br />
-	**[[5ci3]], [[5ci0]], [[5ci1]], [[5ci2]] – EcRNR R2 (mutant) + fluoro-tyrosine + FE<sub>2</sub>O<br />	+
	**[[1w69]] – mRNR R2 + acetate<br />		**[[1w69]] – mRNR R2 + acetate<br />
	**[[6cwp]] – FjRNR + Mn + peptide<br />		**[[6cwp]] – FjRNR + Mn + peptide<br />
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	*Ribonucleotide reductase small+large subunit		*Ribonucleotide reductase small+large subunit

-	**[[3uus]], [[4erm]] - EcRNR R1+ R2<br />	+	**[[3uus]] - EcRNR R1+ R2 + Fe + ATP<br />
-	**[[4erp]] - EcRNR R1+ R2 + ~~inhibitor~~<br />	+	**[[4erm]] - EcRNR R1+ R2 + Fe2O + ATP + ADP<br />
-	**[[2xak]], [[2xap]], [[2xo4]], [[2xo5]] - EcRNR R1+ R2 peptide<BR />	+	**[[4erp]] - EcRNR R1+ R2 + Fe2O + ATP<br />
-	**[[2xav]], [[2xaw]], [[2xax]], [[2xay]], [[2xaz]], [[2x0x]] - EcRNR R1 (mutant) + R2 peptide<BR />	+	**[[2xak]], [[2xap]], [[2xo4]], [[2xo5]] - EcRNR R1 modified+ R2 peptide<BR />
-	**[[5cns]], [[5cnt]], [[5cnv]], [[5cnu]] - EcRNR R1 + R2 + 2 nucleotides<br />	+	**[[2xav]], [[2xaw]], [[2xax]], [[2xay]], [[2xaz]], [[2x0x]] - EcRNR R1 (mutant) modified + R2 peptide<BR />
		+	**[[5cns]], [[5cnt]], [[5cnv]], [[5cnu]] - EcRNR R1 + R2 + Fe2O + 2 nucleotides<br />
		+	**[[2r1r]] - EcRNR R1 + R2 + TTP<BR />
		+	**[[3r1r]] - EcRNR R1 + R2 + AMPPNP<BR />
		+	**[[4r1r]] - EcRNR R1 + R2 + GDP + TTP<BR />
	**[[2bq1]] - StRNR R1+ R2<br />		**[[2bq1]] - StRNR R1+ R2<br />
	**[[5im3]] - RNR + dATP – ''Pseudomonas aeruginosa''<br />		**[[5im3]] - RNR + dATP – ''Pseudomonas aeruginosa''<br />
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	**[[6cgm]] - BaRNR subunit NrdE – ''Bacillus subtilis''<br />		**[[6cgm]] - BaRNR subunit NrdE – ''Bacillus subtilis''<br />
	**[[6cgn]], [[6cgl]] - BaRNR subunit NrdE + AMP derivative <br />		**[[6cgn]], [[6cgl]] - BaRNR subunit NrdE + AMP derivative <br />
		+	**[[1pem]] - StRNR NrdE – Salmonella typhimurium<br />
		+	**[[1peo]], [[1peq]], [[1peu]] - StRNR NrdE + nucleotide<br />
		+	**[[2bq1]] - StRNR NrdE + NrdF + Fe + GTP<br />
	**[[4dr0]] - BaRNR subunit NrdF + Mn <br />		**[[4dr0]] - BaRNR subunit NrdF + Mn <br />
	**[[4bmq]], [[4bmr]], [[4bmt]] - BcRNR NrdF + Fe – ''Bacillus cereus''<br />		**[[4bmq]], [[4bmr]], [[4bmt]] - BcRNR NrdF + Fe – ''Bacillus cereus''<br />
	**[[4bmu]] - BcRNR NrdF + Mn<br />		**[[4bmu]] - BcRNR NrdF + Mn<br />
	**[[4bmo]], [[4bmp]] - BcRNR NrdF + NrdI + Fe + FMN<br />		**[[4bmo]], [[4bmp]] - BcRNR NrdF + NrdI + Fe + FMN<br />
		+	**[[4m1f]] - EcRNR NrdF<br />
		+	**[[3n37]] - EcRNR NrdF + Mn<br />
		+	**[[3n38]] - EcRNR NrdF + Fe<br />
		+	**[[3n39]], [[3n3a]] - EcRNR NrdF + NrdI + Mn + FMN<br />
		+	**[[3n3b]] - EcRNR NrdF + NrdI + Mn + FMN + Fe2O<br />
		+	**[[4n82]] – SsRNR + FMN – ''Streptococcus sanguinis''<br />
		+	**[[4n83]] - SsRNR NrdF + Mn<br />
		+	**[[1r2f]] - StRNR NrdF + Fe<br />
		+	**[[2r2f]] - StRNR NrdF + Fe2O<br />
		+	**[[3mjo]] - CcRNR NrdF + Mn - ''Corynebacterium ammoniagenes'' <br />
		+	**[[1kgn]], [[1kgo]], [[1kgp]], [[1oqu]], [[3dhz]] - CcRNR NrdF + Fe<br />

	*'''Class II ribonucleotide reductase'''		*'''Class II ribonucleotide reductase'''
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	**[[3o0o]] - TmRNR + TTP + GDP + Mg + deoxyadenosine + B12<br />		**[[3o0o]] - TmRNR + TTP + GDP + Mg + deoxyadenosine + B12<br />
	**[[3o0q]] - TmRNR + TTP + GDP + Mg + adenosine <br />		**[[3o0q]] - TmRNR + TTP + GDP + Mg + adenosine <br />
-	**[[1pem]] - StRNR R1 <BR />
-	**[[1r2f]], [[2r2f]] - StRNR R2<br />
-	**[[1peo]], [[1peq]], [[2peu]] - StRNR R1 + effector<BR />
	**[[1l1l]] – RNR (mutant) – ''Lactobacillus leichmannii''<br />		**[[1l1l]] – RNR (mutant) – ''Lactobacillus leichmannii''<br />

Michal Harel at 08:27, 15 October 2018

Michal Harel — Mon, 15 Oct 2018 08:27:56 GMT

←Older revision		Revision as of 08:27, 15 October 2018
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	== Function ==		== Function ==
	'''Ribonucleotide reductase''' (RNR) or '''ribonucleotide-diphosphate reductase''' catalyzes the formation of deoxyribonucleotides from ribonucleotides<ref>PMID:16756507</ref>. There are 3 classes of RNR.<br />		'''Ribonucleotide reductase''' (RNR) or '''ribonucleotide-diphosphate reductase''' catalyzes the formation of deoxyribonucleotides from ribonucleotides<ref>PMID:16756507</ref>. There are 3 classes of RNR.<br />
-	* '''Class I RNR''' is a tetramer composed from large (RNR1) and small (RNR2) subunits. Class I RNR is iron-dependent and produces tyrosyl radical. Thimidine triphosphate (TTP) is an effector in the reaction.<br />	+	* '''Class I RNR''' is a tetramer composed from large (RNR1) and small (RNR2) subunits. Class I RNR is iron-dependent and produces tyrosyl radical. Thimidine triphosphate (TTP) is an effector in the reaction<ref>PMID:21456967</ref>.<br />
-	* ''' Class Ib RNR''' contains 2 proteins: α (NrdE) and β (NrdF).<br />	+	* ''' Class Ib RNR''' contains 2 proteins: α (NrdE) and β (NrdF)<ref>PMID:21250660</ref>.<br />
-	* ''' Class II RNR''' reduces ribonucleotide triphosphates using coenzyme B12.<br />	+	* ''' Class II RNR''' reduces ribonucleotide triphosphates using coenzyme B12<ref>PMID:11875520</ref>.<br />
-	* '''Class III RNR''' generate glycine radical using S-adenosyl methionine and Fe-S center.<br />	+	* '''Class III RNR''' generate glycine radical using S-adenosyl methionine and Fe-S center<ref>PMID:17606358</ref>.<br />
	For details on human RNR2 see [[P53R2]].<br />		For details on human RNR2 see [[P53R2]].<br />
	For mouse RNR see [[Mouse Ribonucleotide Reductase R2]].<br />		For mouse RNR see [[Mouse Ribonucleotide Reductase R2]].<br />