Ribonucleotide reductase

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 18: Line 18:
*<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>
Line 30: Line 34:
**[[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 />
Line 56: Line 60:
*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 />
Line 62: Line 71:
**[[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 />
Line 85: Line 88:
*''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
Line 106: Line 116:
**[[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 />
Line 124: Line 141:
**[[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'''

Revision as of 09:48, 16 December 2019

Class II ribonucleotide reductase dimer complex with dATP, UDP and Mg+2 ion (green) (PDB entry 1xjg)

Drag the structure with the mouse to rotate

3D Structures of Ribonucleotide reductase

Updated on 16-December-2019

References

  1. ↑ Nordlund P, Reichard P. Ribonucleotide reductases. Annu Rev Biochem. 2006;75:681-706. PMID:16756507 doi:http://dx.doi.org/10.1146/annurev.biochem.75.103004.142443
  2. ↑ Cotruvo JA, Stubbe J. Class I ribonucleotide reductases: metallocofactor assembly and repair in vitro and in vivo. Annu Rev Biochem. 2011;80:733-67. doi: 10.1146/annurev-biochem-061408-095817. PMID:21456967 doi:http://dx.doi.org/10.1146/annurev-biochem-061408-095817
  3. ↑ Cotruvo JA, Stubbe J. Escherichia coli class Ib ribonucleotide reductase contains a dimanganese(III)-tyrosyl radical cofactor in vivo. Biochemistry. 2011 Mar 15;50(10):1672-81. doi: 10.1021/bi101881d. Epub 2011 Feb, 15. PMID:21250660 doi:http://dx.doi.org/10.1021/bi101881d
  4. ↑ Torrents E, Grinberg I, Gorovitz-Harris B, Lundstrom H, Borovok I, Aharonowitz Y, Sjoberg BM, Cohen G. NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. J Bacteriol. 2007 Jul;189(14):5012-21. Epub 2007 May 11. PMID:17496099 doi:http://dx.doi.org/JB.00440-07
  5. ↑ Sintchak MD, Arjara G, Kellogg BA, Stubbe J, Drennan CL. The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer. Nat Struct Biol. 2002 Apr;9(4):293-300. PMID:11875520 doi:http://dx.doi.org/10.1038/nsb774
  6. ↑ Kirdis E, Jonsson IM, Kubica M, Potempa J, Josefsson E, Masalha M, Foster SJ, Tarkowski A. Ribonucleotide reductase class III, an essential enzyme for the anaerobic growth of Staphylococcus aureus, is a virulence determinant in septic arthritis. Microb Pathog. 2007 Nov-Dec;43(5-6):179-88. doi: 10.1016/j.micpath.2007.05.008., Epub 2007 May 25. PMID:17606358 doi:http://dx.doi.org/10.1016/j.micpath.2007.05.008
  7. ↑ Munro JB, Silva JC. Ribonucleotide reductase as a target to control apicomplexan diseases. Curr Issues Mol Biol. 2012;14(1):9-26. Epub 2011 Jul 26. PMID:21791713
  8. ↑ Larsson KM, Jordan A, Eliasson R, Reichard P, Logan DT, Nordlund P. Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase. Nat Struct Mol Biol. 2004 Nov;11(11):1142-9. Epub 2004 Oct 10. PMID:15475969 doi:http://dx.doi.org/10.1038/nsmb838

Proteopedia Page Contributors and Editors (what is this?)

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

Retrieved from "http://52.214.119.220/wiki/index.php/Ribonucleotide_reductase"
Personal tools