Ribonucleotide reductase: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Jaime Prilusky, Alexander Berchansky, Joel L. Sussman

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-<StructureSection load='1xjg' size='450' side='right' caption='Class II ribonucleotide reductase dimer complex with dATP, UDP (stick models) and Mg+2 ion (green) (PDB entry [[1xjg]])' scene='46/461381/Cv/1'>
+<StructureSection load='' size='350' side='right' caption='Class II ribonucleotide reductase dimer complex with dATP, UDP and Mg+2 ion (green) (PDB entry [[1xjg]])' scene='46/461381/Cv/1'>
 == Function ==
-'''Ribonucleotide reductase''' (RNR) 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 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 II RNR''' reduces ribonucleotide triphosphates using coenzyme B12.<br />
+*  ''' Class Ib RNR''' contains 2 proteins: α (NrdE) and β (NrdF)<ref>PMID:21250660</ref>.<br />
-*  '''Class III RNR''' generate glycine radical using S-adenosyl methionine and Fe-S center.<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 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 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 ==
@@ Line 13: / Line 16: @@
 == Structural highlights ==
-Class II RNR is vitamin B12-dependent.  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>.
-</StructureSection>
+*<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>.
 == 3D Structures of Ribonucleotide reductase ==
+[[Ribonucleotide reductase 3D structures]]
-Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
+</StructureSection>
-{{#tree:id=OrganizedByTopic|openlevels=0|
-*'''Class I ribonucleotide reductase'''
-*Ribonucleotide reductase large subunit
-**[[1zyz]], [[1zzd]], [[2cvs]], [[2cvt]], [[2cvu]], [[2cvv]], [[2cvw]], [[2cvx]], [[2cvy]] - yRNR R1 – yeast<BR />
-**[[5r1r]], [[6r1r]], [[7r1r]], [[1r1r]], [[1rlr]], [[1mrr]] - EcRNR R1 – ''Escherichia coli''<br />
-**[[4n82]] – SsRNR – ''Streptococcus sanguinis''<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 />
-**[[4x3v]] - hRNR M1 + inhibitor<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 + inhibitor<br />
-**[[2r1r]] - EcRNR R1 + TTP<BR />
-**[[3r1r]] - EcRNR R1 + AMPPNP<BR />
-**[[4r1r]] - EcRNR R1 + GDP + TTP<BR />
-**[[1qfn]] - EcRNR R1 + glutaredoxin 1<br />
-**[[1peu]] - StRNR + DTP - ''Salmonella typhimurium''<br />
-*RNR small subunit
-**[[2xof]], [[3n37]], [[3n38]], [[2alx]], [[1piy]], [[1r65]], [[1mxr]], [[1jqc]], [[1jpr]], [[1av8]], [[1xik]], [[1rib]], [[4m1f]] – EcRNR R2 <BR />
-**[[1yfd]], [[1piz]], [[1pj0]], [[1pj1]], [[1pm2]], [[1pim]], [[1piu]], [[1biq]], [[2av8]], [[1pfr]] - EcRNR R2 (mutant) + Fe<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 />
-**[[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 />
-**[[1syy]] - CtRNR R2 + Fe + Pb– ''Chlamydia trachomatis''<BR />
-**[[2ani]] - CtRNR R2 (mutant) + Fe + Pb<BR />
-**[[4m1h]] - CtRNR R2 <br />
-**[[4dr0]] - RNR + Mn – Bacillus subtilis<br />
-**[[1uzr]] – RNR 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 />
-**[[4bmq]], [[4bmr]], [[4bmt]] - BcRNR + Fe – ''Bacillus cereus''<br />
-**[[4bmu]] - BcRNR + Mn<br />
-**[[4n83]] - SsRNR + Mn<br />
-*''Ribonucleotide reductase small subunit complex''
-**[[1rsr]], [[1rsv]] - EcRNR R2 (mutant) + N3<BR />
-**[[3n39]], [[3n3a]], [[3n3b]] – EcRNR R2 + NrdI<BR />
-**[[1rnr]] – EcRNR R2 (mutant) + dopa<BR />
-**[[5ci4]] – EcRNR R2 (mutant) + FE2O<br />
-**[[5ci3]], [[5ci0]], [[5ci1]], [[5ci2]] – EcRNR R2 (mutant) + fluoro-tyrosine + FE<sub>2</sub>O<br />
-**[[1w69]] – mRNR R2 + acetate<br />
-**[[4bmo]], [[4bmp]] - BcRNR + NrdI <br />
-*Ribonucleotide reductase small+large subunit
-**[[3uus]], [[4erm]] - EcRNR R1+ R2<br />
-**[[4erp]] - EcRNR R1+ R2 + inhibitor<br />
-**[[2xak]], [[2xap]], [[2xo4]], [[2xo5]] - EcRNR R1+ R2 peptide<BR />
-**[[2xav]], [[2xaw]], [[2xax]], [[2xay]], [[2xaz]], [[2x0x]] - EcRNR R1 (mutant) + R2 peptide<BR />
-**[[5cns]], [[5cnt]], [[5cnv]], [[5cnu]] - EcRNR R1 + R2 + 2 nucleotides<br />
-**[[2bq1]] - StRNR R1+ R2<br />
-**[[5im3]] - RNR + dATP – ''Pseudomonas aeruginosa''<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 />
-**[[1pem]] - StRNR R1 <BR />
-**[[1r2f]], [[2r2f]] - StRNR R2<br />
-**[[1peo]], [[1peq]], [[2peu]] - StRNR R1 + effector<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/>
 [[Category:Topic Page]]