DB code: M00205
| CATH domain | 1.-.-.- : | |
|---|---|---|
| 1.10.395.10 : | ||
| 3.90.244.10 : | Catalytic domain | |
| 3.90.188.10 : | Catalytic domain | |
| -.-.-.- : | ||
| 1.10.620.20 : Ribonucleotide Reductase, subunit A | Catalytic domain | |
| E.C. | 1.17.4.1 | |
| CSA | ||
| M-CSA | ||
| MACiE | ||
| CATH domain | Related DB codes (homologues) |
|---|---|
| 1.10.620.20 : Ribonucleotide Reductase, subunit A | S00028 M00151 M00204 |
| 3.90.188.10 : | M00204 |
| 3.90.244.10 : | M00204 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | Pfam |
|---|---|---|---|---|
| P21524 |
Ribonucleoside-diphosphate reductase large chain 1
|
EC
1.17.4.1
Ribonucleotide reductase large subunit 1 Ribonucleotide reductase R1 subunit 1 |
NP_010993.1
(Protein)
NM_001178961.1 (DNA/RNA sequence) |
PF03477
(ATP-cone)
PF02867 (Ribonuc_red_lgC) PF00317 (Ribonuc_red_lgN) [Graphical View] |
| P21672 |
Ribonucleoside-diphosphate reductase large chain 2
|
EC
1.17.4.1
Ribonucleotide reductase large subunit 2 Ribonucleotide reductase DNA damage-inducible regulatory subunit 2 Ribonucleotide reductase R1 subunit 2 |
NP_012198.3
(Protein)
NM_001179416.3 (DNA/RNA sequence) |
PF03477
(ATP-cone)
PF02867 (Ribonuc_red_lgC) PF00317 (Ribonuc_red_lgN) [Graphical View] |
| P09938 |
Ribonucleoside-diphosphate reductase small chain 1
|
EC
1.17.4.1
Ribonucleotide reductase small subunit 1 Ribonucleotide reductase R2 subunit 1 |
NP_012508.1
(Protein)
NM_001181460.1 (DNA/RNA sequence) |
PF00268
(Ribonuc_red_sm)
[Graphical View] |
| P49723 |
Ribonucleoside-diphosphate reductase small chain 2
|
EC
1.17.4.1
Ribonucleotide reductase small subunit 2 Ribonucleotide reductase R2 subunit 2 |
NP_011696.3
(Protein)
NM_001181309.3 (DNA/RNA sequence) |
PF00268
(Ribonuc_red_sm)
[Graphical View] |
| KEGG enzyme name |
|---|
|
ribonucleoside-diphosphate reductase
ribonucleotide reductase CDP reductase ribonucleoside diphosphate reductase UDP reductase ADP reductase nucleoside diphosphate reductase ribonucleoside 5'-diphosphate reductase ribonucleotide diphosphate reductase 2'-deoxyribonucleoside-diphosphate:oxidized-thioredoxin2'-oxidoreductase RR |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P21524 | RIR1_YEAST | 2''-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin. | Heterotetramer of two large (R1) and two small (R2) subunits. S.cerevisiae has two different R1 subunits (RNR1 and RNR3) and two different R2 subunits (RNR2 and RNR4). The functional form of the small subunits is a RNR2-RNR4 heterodimer, where RNR2 provides the iron-radical center and RNR4 is required for proper folding of RNR2 and assembly with the large subunits. Under normal growth conditions, the active form of the large subunits is a homodimer of the constitutively expressed RNR1. In damaged cells or cells arrested for DNA synthesis, the reductase consists of multiple species because of the association of the small subunits (RNR2-RNR4) with either the RNR1 homodimer or a heterodimer of RNR1 and the damage-inducible RNR3. RNR1 interacts with the ribonucleotide reductase inhibitor SML1. | Cytoplasm. | |
| P21672 | RIR3_YEAST | 2''-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin. | Heterotetramer of two large (R1) and two small (R2) subunits. S.cerevisiae has two different R1 subunits (RNR1 and RNR3) and two different R2 subunits (RNR2 and RNR4). The functional form of the small subunits is a RNR2-RNR4 heterodimer, where RNR2 provides the iron-radical center and RNR4 is required for proper folding of RNR2 and assembly with the large subunits. Under normal growth conditions, the active form of the large subunits is a homodimer of the constitutively expressed RNR1. In damaged cells or cells arrested for DNA synthesis, the reductase consists of multiple species because of the association of the small subunits (RNR2-RNR4) with either the RNR1 homodimer or a heterodimer of RNR1 and the damage-inducible RNR3. | Cytoplasm. | |
| P09938 | RIR2_YEAST | 2''-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin. | Heterotetramer of two large (R1) and two small (R2) subunits. S.cerevisiae has two different R1 subunits (RNR1 and RNR3) and two different R2 subunits (RNR2 and RNR4). The functional form of the small subunits is a RNR2-RNR4 heterodimer, where RNR2 provides the iron-radical center and RNR4 is required for proper folding of RNR2 and assembly with the large subunits. Under normal growth conditions, the active form of the large subunits is a homodimer of the constitutively expressed RNR1. In damaged cells or cells arrested for DNA synthesis, the reductase consists of multiple species because of the association of the small subunits (RNR2-RNR4) with either the RNR1 homodimer or a heterodimer of RNR1 and the damage-inducible RNR3. | Nucleus. Note=Found predominantly in the nucleus under normal growth conditions and is redistributed to the cytoplasm in damaged cells in a DNA replication and damage checkpoint-dependent manner. | Binds 2 iron ions per subunit. |
| P49723 | RIR4_YEAST | 2''-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin. | Heterotetramer of two large (R1) and two small (R2) subunits. S.cerevisiae has two different R1 subunits (RNR1 and RNR3) and two different R2 subunits (RNR2 and RNR4). The functional form of the small subunits is a RNR2-RNR4 heterodimer, where RNR2 provides the iron-radical center and RNR4 is required for proper folding of RNR2 and assembly with the large subunits. Under normal growth conditions, the active form of the large subunits is a homodimer of the constitutively expressed RNR1. In damaged cells or cells arrested for DNA synthesis, the reductase consists of multiple species because of the association of the small subunits (RNR2-RNR4) with either the RNR1 homodimer or a heterodimer of RNR1 and the damage-inducible RNR3. | Nucleus. Note=Found predominantly in the nucleus under normal growth conditions and is redistributed to the cytoplasm in damaged cells in a DNA replication and damage checkpoint-dependent manner. |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00230 | Purine metabolism | |
| MAP00240 | Pyrimidine metabolism | |
| MAP00480 | Glutathione metabolism |
| Compound table | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cofactors | Substrates | Products | Intermediates | ||||||||||
| KEGG-id | C00023 | C00002 | C00342 | C03723 | C04232 | C00343 | C00001 | ||||||
| E.C. | |||||||||||||
| Compound | Iron | ATP | Reduced thioredoxin | Ribonucleoside diphosphate | 2'-Deoxyribonucleoside diphosphate | Oxidized thioredoxin | H2O | ||||||
| Type | heavy metal | amine group,nucleotide | amide group,carbohydrate,peptide/protein,sulfhydryl group | nucleotide | nucleotide | amide group,carbohydrate,disulfide bond,peptide/protein | H2O | ||||||
| ChEBI |
18248 82664 18248 82664 |
15422 15422 |
15377 15377 |
||||||||||
| PubChem |
23925 23925 |
5957 5957 |
22247451 962 22247451 962 |
||||||||||
| 1zyzA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1zyzB01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvsA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvtA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvxA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1zyzA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1zyzB02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1zzdA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvsA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvtA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvuA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvvA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvwA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvxA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvyA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2eudA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1zyzA03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1zyzB03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1zzdA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvsA03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvtA03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvuA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Bound:CDP | Unbound | Unbound | ||
| 2cvvA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Bound:UDP | Unbound | Unbound | ||
| 2cvwA02 |
|
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|
|
Unbound | Unbound | Unbound | Bound:GDP | Unbound | Unbound | ||
| 2cvxA03 |
|
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Unbound | Unbound | Unbound | Bound:ADP | Unbound | Unbound | ||
| 2cvyA02 |
|
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2eudA02 |
|
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|
Unbound | Unbound | Unbound | Analogue:GCQ | Unbound | Unbound | ||
| 1zyzA04 |
|
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1zyzB04 |
|
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|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1zzdA03 |
|
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|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvsA04 |
|
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|
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2cvtA04 |
|
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Unbound | Analogue:ANP | Unbound | Unbound | Unbound | Unbound | ||
| 2cvuA03 |
|
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Unbound | Analogue:ANP | Unbound | Unbound | Unbound | Unbound | ||
| 2cvvA03 |
|
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Unbound | Analogue:ANP | Unbound | Unbound | Unbound | Unbound | ||
| 2cvwA03 |
|
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Unbound | Analogue:TTP | Unbound | Unbound | Unbound | Unbound | ||
| 2cvxA04 |
|
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Unbound | Analogue:DGT | Unbound | Unbound | Unbound | Unbound | ||
| 2cvyA03 |
|
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Unbound | Analogue:TTP | Unbound | Unbound | Unbound | Unbound | ||
| 2eudA03 |
|
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|
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Unbound | Analogue:ANP | Unbound | Unbound | Unbound | Unbound | ||
| 1jk0A |
|
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Analogue:_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1smqA |
|
|
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|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1smqB |
|
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|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1smqC |
|
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1smqD |
|
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1jk0B |
|
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|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1smsA |
|
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1smsB |
|
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|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| PDB;2r1r, 3r1r & Swiss-prot;P00452 & literature [14] | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1zyzA01 |
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| 1zyzB01 |
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| 2cvsA01 |
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| 2cvtA01 |
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| 2cvxA01 |
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| 1zyzA02 |
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| 1zyzB02 |
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| 1zzdA01 |
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| 2cvsA02 |
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| 2cvtA02 |
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| 2cvuA01 |
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| 2cvvA01 |
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| 2cvwA01 |
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| 2cvxA02 |
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|||||
| 2cvyA01 |
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|||||
| 2eudA01 |
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| 1zyzA03 |
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TYR 741;TYR 742 | ||||
| 1zyzB03 |
|
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TYR 741;TYR 742 | ||||
| 1zzdA02 |
|
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TYR 741;TYR 742 | ||||
| 2cvsA03 |
|
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TYR 741;TYR 742 | ||||
| 2cvtA03 |
|
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TYR 741;TYR 742 | ||||
| 2cvuA02 |
|
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TYR 741;TYR 742 | ||||
| 2cvvA02 |
|
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TYR 741;TYR 742 | ||||
| 2cvwA02 |
|
|
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TYR 741;TYR 742 | ||||
| 2cvxA03 |
|
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|
TYR 741;TYR 742 | ||||
| 2cvyA02 |
|
|
|
|
|
TYR 741;TYR 742 | ||||
| 2eudA02 |
|
|
|
|
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TYR 741;TYR 742 | ||||
| 1zyzA04 |
|
|
|
|
|
CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | ||||
| 1zyzB04 |
|
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|
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CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | ||||
| 1zzdA03 |
|
|
|
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|
CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | disulfide bonded/oxidized form C218-C443 | |||
| 2cvsA04 |
|
|
|
|
|
CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | disulfide bonded/oxidized form C218-C443 | |||
| 2cvtA04 |
|
|
|
|
|
CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | ||||
| 2cvuA03 |
|
|
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|
|
CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | ||||
| 2cvvA03 |
|
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|
|
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CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | ||||
| 2cvwA03 |
|
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|
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|
CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | ||||
| 2cvxA04 |
|
|
|
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|
CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | ||||
| 2cvyA03 |
|
|
|
|
|
CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | disulfide bonded/oxidized form C218-C443 | |||
| 2eudA03 |
|
|
|
|
|
CYS 218;ASN 426;CYS 428;GLU 430;CYS 443 | ||||
| 1jk0A |
|
|
|
|
|
TYR 183 | ASP 145;HIS 179(Iron-1);GLU 239;HIS 276(Iron-2);GLU 176;GLU 273(both Iron-1 & Iron-2) | |||
| 1smqA |
|
|
|
|
|
TYR 183 | ;HIS 179(Iron-1);GLU 239;HIS 276(Iron-2);GLU 176;GLU 273(both Iron-1 & Iron-2) | invisible 145-149 | ||
| 1smqB |
|
|
|
|
|
TYR 183 | ;HIS 179(Iron-1);GLU 239;HIS 276(Iron-2);GLU 176;GLU 273(both Iron-1 & Iron-2) | invisible 145-149 | ||
| 1smqC |
|
|
|
|
|
TYR 183 | ;HIS 179(Iron-1);GLU 239;HIS 276(Iron-2);GLU 176;GLU 273(both Iron-1 & Iron-2) | invisible 145-149 | ||
| 1smqD |
|
|
|
|
|
TYR 183 | ;HIS 179(Iron-1);GLU 239;HIS 276(Iron-2);GLU 176;GLU 273(both Iron-1 & Iron-2) | invisible 145-149 | ||
| 1jk0B |
|
|
|
|
|
TYR 131 | ||||
| 1smsA |
|
|
|
|
|
TYR 131 | ||||
| 1smsB |
|
|
|
|
|
TYR 131 | ||||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[3]
|
Scheme I, p.12750 | |
|
[3]
|
Scheme II, p.12750 | |
|
[3]
|
Scheme III, p.12751 | |
|
[7]
|
FIG. 4c, p.537 | |
|
[9]
|
Scheme 1, p.8382 | |
|
[9]
|
Scheme 2, p.8389 | |
|
[9]
|
Scheme 3, p.8389 | |
|
[9]
|
Scheme 4, p.8389 | |
|
[10]
|
FScheme 2, p.10066 | |
|
[13]
|
FIG. 2, p.31534 | |
|
[14]
|
Figure 9, p.1088 | |
|
[23]
|
SCHEME 1, p.60 | |
|
[25]
|
SCHEME 1, p.5750 | |
|
[25]
|
SCHEME 2, p.5752 | |
|
[26]
|
Figure 3, p.313 | |
|
[26]
|
Figure 4, p.314 | |
|
[26]
|
Figure 7, p.316 | |
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | Subunit R2 |
| Medline ID | |
| PubMed ID | 1963165 |
| Journal | Free Radic Res Commun |
| Year | 1990 |
| Volume | 10 |
| Pages | 281-6 |
| Authors | Harder J, Follmann H |
| Title | Identification of a free radical and oxygen dependence of ribonucleotide reductase in yeast. |
| Related PDB | |
| Related UniProtKB | |
| [2] | |
| Resource | |
| Comments | Subunit R1 |
| Medline ID | |
| PubMed ID | 11074005 |
| Journal | Mol Cell Biol |
| Year | 2000 |
| Volume | 20 |
| Pages | 9076-83 |
| Authors | Zhao X, Georgieva B, Chabes A, Domkin V, Ippel JH, Schleucher J, Wijmenga S, Thelander L, Rothstein R |
| Title | Mutational and structural analyses of the ribonucleotide reductase inhibitor Sml1 define its Rnr1 interaction domain whose inactivation allows suppression of mec1 and rad53 lethality. |
| Related PDB | |
| Related UniProtKB | |
| [3] | |
| Resource | |
| Comments | Subunit R2 |
| Medline ID | |
| PubMed ID | 11472128 |
| Journal | J Am Chem Soc |
| Year | 2001 |
| Volume | 123 |
| Pages | 3569-76 |
| Authors | Bar G, Bennati M, Nguyen HH, Ge J, Stubbe JA, Griffin RG |
| Title | High-frequency (140-GHz) time domain EPR and ENDOR spectroscopy: the tyrosyl radical-diiron cofactor in ribonucleotide reductase from yeast. |
| Related PDB | |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments |
X-ray crystallography, |
| Medline ID | |
| PubMed ID | 11526233 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 2001 |
| Volume | 98 |
| Pages | 10073-8 |
| Authors | Voegtli WC, Ge J, Perlstein DL, Stubbe J, Rosenzweig AC |
| Title | Structure of the yeast ribonucleotide reductase Y2Y4 heterodimer. |
| Related PDB | 1jk0 |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments |
X-ray crystallography, |
| Medline ID | |
| PubMed ID | 15196016 |
| Journal | Biochemistry |
| Year | 2004 |
| Volume | 43 |
| Pages | 7736-42 |
| Authors | Sommerhalter M, Voegtli WC, Perlstein DL, Ge J, Stubbe J, Rosenzweig AC |
| Title | Structures of the yeast ribonucleotide reductase Rnr2 and Rnr4 homodimers. |
| Related PDB | 1smq 1sms |
| Related UniProtKB | |
| [6] | |
| Resource | |
| Comments | Subunit R1 |
| Medline ID | |
| PubMed ID | 16537479 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 2006 |
| Volume | 103 |
| Pages | 4022-7 |
| Authors | Xu H, Faber C, Uchiki T, Fairman JW, Racca J, Dealwis C |
| Title | Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation. |
| Related PDB | 1zyz 1zzd 2cvs 2cvt 2cvu 2cvv 2cvw 2cvx 2cvy |
| Related UniProtKB | |
| [7] | |
| Resource | |
| Comments | Subunit R1 |
| Medline ID | |
| PubMed ID | 16537480 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 2006 |
| Volume | 103 |
| Pages | 4028-33 |
| Authors | Xu H, Faber C, Uchiki T, Racca J, Dealwis C |
| Title | Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly. |
| Related PDB | 2eud |
| Related UniProtKB | |
| Comments |
|---|
|
(C) Electron transfer from the active site redox-active cysteine pair (Cys218 & Cys443) to the substrate nucleotide.
This enzyme belongs to the class I ribonucleotide reductases (RNR). The functional form of the small subunits is a RNR2-RNR4 heterodimer, Futhermore, The class Ia enzyme has got a allosteric regulation by ATP. According to the counterpart enzyme from Salmonella typhimurium (M00204 in EzCatDB), (A) Electron transfer from thioredoxin (an external donor) to the redox-active Cys883-Cys886 of RNR1 (or Cys864-Cys867 of RNR3) (disulfide) at the C-terminus of the R1 subunit. (B) Electron transfer from the C-terminus redox-active cysteine pair to the active site redox-active Cys218-Cys443. (D) Radical formation at Tyr183 of the R2 subunit (RNR2): (E) Radical transfer from Tyr183 to the di-iron site of the R2 subunit (RNR2). (F) Radical transfer from the di-iron site to the active site Cys428, (G) Radical reaction for the substrate nucleotide at the active site Cys428. ##### Other classes are as follows: Class I enzymes: M00011 (class Ia), Clsss II enzyme (e.g. Class III enzyme (E.C. |
| Created | Updated |
|---|---|
| 2004-03-25 | 2009-02-26 |