Ribonucleoside-diphosphate reductase 1 subunit beta (P69924)

Identification
Name:Ribonucleoside-diphosphate reductase 1 subunit beta
Synonyms:
  • Protein B2
  • Protein R2
  • Ribonucleotide reductase 1
Gene Name:nrdB
Enzyme Class:
Biological Properties
General Function:Involved in oxidoreductase activity
Specific Function:Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis
Cellular Location:Not Available
SMPDB Pathways:
KEGG Pathways:
KEGG Reactions:
1.0Thumb+1.0Thioredoxin disulfide+1.0Thumb ↔ 1.0Thioredoxin+1.0Thumb
1.0dADP + 1.0Thioredoxin disulfide + 1.0Water ↔ 1.0Thioredoxin + 1.0ADP
ReactionCard
1.0dUDP+1.0Thioredoxin disulfide+1.0Thumb ↔ 1.0Thioredoxin+1.0Thumb
1.0dUDP + 1.0Thioredoxin disulfide + 1.0Water ↔ 1.0Thioredoxin + 1.0Uridine 5'-diphosphate
ReactionCard
1.0dGDP+1.0Thioredoxin disulfide+1.0Thumb ↔ 1.0Thumb+1.0Thioredoxin
1.0dGDP + 1.0Thioredoxin disulfide + 1.0Water ↔ 1.0Guanosine diphosphate + 1.0Thioredoxin
ReactionCard
1.0Thumb+1.0Thioredoxin disulfide+1.0Thumb ↔ 1.0Thioredoxin+1.0Thumb
1.0dCDP + 1.0Thioredoxin disulfide + 1.0Water ↔ 1.0Thioredoxin + 1.0CDP
ReactionCard
1.02'-Deoxyribonucleoside diphosphate+1.0Thioredoxin disulfide+1.0Thumb ↔ 1.0Ribonucleoside diphosphate+1.0Thumb
1.02'-Deoxyribonucleoside diphosphate + 1.0Thioredoxin disulfide + 1.0Water ↔ 1.0Ribonucleoside diphosphate + 1.0Thioredoxin
ReactionCard
SMPDB Reactions:
1.0Thumb+1.0reduced thioredoxin → 1.0oxidized thioredoxin +1.0Thumb+1.0dGDP+1.0Thumb
1.0Guanosine diphosphate + 1.0reduced thioredoxin → 1.0oxidized thioredoxin + 1.0Water + 1.0dGDP + 1.0dGDP
ReactionCard
1.0Adenosine diphosphate+1.0reduced thioredoxin+1.0Thumb ↔ 1.0Thumb+1.0oxidized thioredoxin +1.0dADP+1.0Thumb
1.0Adenosine diphosphate + 1.0reduced thioredoxin + 1.0ADP ↔ 1.0Water + 1.0oxidized thioredoxin + 1.0dADP + 1.0dADP
ReactionCard
1.0Uridine 5'-diphosphate+1.0reduced thioredoxin+1.0Thumb ? 1.0oxidized thioredoxin +1.0Thumb+1.0dUDP+1.0Thumb
1.0Uridine 5'-diphosphate + 1.0reduced thioredoxin + 1.0Uridine 5'-diphosphate ? 1.0oxidized thioredoxin + 1.0Water + 1.0dUDP + 1.0dUDP
ReactionCard
1.0Thumb+1.0reduced thioredoxin → 1.0Thumb+1.0oxidized thioredoxin +1.0Thumb
1.0CDP + 1.0reduced thioredoxin → 1.0Water + 1.0oxidized thioredoxin + 1.0dCDP
ReactionCard
Complex Reactions:
1.0Thumb+1.0Reduced Thioredoxin → 1.0Thumb+1.0Thumb+1.0Oxidized Thioredoxin
1.0ADP + 1.0Reduced Thioredoxin → 1.0dADP + 1.0Water + 1.0Oxidized Thioredoxin
ReactionCard
1.0Thumb+1.0Reduced Thioredoxin → 1.0Thumb+1.0Thumb+1.0Oxidized Thioredoxin
1.0Guanosine diphosphate + 1.0Reduced Thioredoxin → 1.0dGDP + 1.0Water + 1.0Oxidized Thioredoxin
ReactionCard
1.0Thumb+1.0Reduced Thioredoxin → 1.0Thumb+1.0Thumb+1.0Oxidized Thioredoxin
1.0CDP + 1.0Reduced Thioredoxin → 1.0dCDP + 1.0Water + 1.0Oxidized Thioredoxin
ReactionCard
1.0Reduced Thioredoxin+1.0Thumb → 1.0Thumb+1.0Thumb+1.0Oxidized Thioredoxin
1.0Reduced Thioredoxin + 1.0Uridine 5'-diphosphate → 1.0dUDP + 1.0Water + 1.0Oxidized Thioredoxin
ReactionCard
Metabolites:
ECMDB IDNameView
ECMDB01341ADPMetaboCard
ECMDB01546CDPMetaboCard
ECMDB21326dADPMetaboCard
ECMDB01245dCDPMetaboCard
ECMDB00960dGDPMetaboCard
ECMDB01000dUDPMetaboCard
ECMDB01201Guanosine diphosphateMetaboCard
ECMDB23749ThioredoxinMetaboCard
ECMDB00295Uridine 5'-diphosphateMetaboCard
ECMDB00494WaterMetaboCard
GO Classification:
Function
binding
catalytic activity
cation binding
ion binding
metal ion binding
oxidoreductase activity
oxidoreductase activity, acting on CH or CH2 groups
oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor
ribonucleoside-diphosphate reductase activity
transition metal ion binding
Process
cellular nitrogen compound metabolic process
deoxyribonucleoside diphosphate metabolic process
metabolic process
nitrogen compound metabolic process
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleoside diphosphate metabolic process
nucleoside phosphate metabolic process
nucleotide metabolic process
oxidation reduction
Gene Properties
Blattner:b2235
Gene OrientationClockwise
Centisome Percentage:50.55
Left Sequence End2345406
Right Sequence End2346536
Gene Sequence:
>1131 bp
ATGGCTAAGCAAGATTATTACGAGATTTTAGGCGTTTCCAAAACAGCGGAAGAGCGTGAA
ATCAGAAAGGCCTACAAACGCCTGGCCATGAAATACCACCCGGACCGTAACCAGGGTGAC
AAAGAGGCCGAGGCGAAATTTAAAGAGATCAAGGAAGCTTATGAAGTTCTGACCGACTCG
CAAAAACGTGCGGCATACGATCAGTATGGTCATGCTGCGTTTGAGCAAGGTGGCATGGGC
GGCGGCGGTTTTGGCGGCGGCGCAGACTTCAGCGATATTTTTGGTGACGTTTTCGGCGAT
ATTTTTGGCGGCGGACGTGGTCGTCAACGTGCGGCGCGCGGTGCTGATTTACGCTATAAC
ATGGAGCTCACCCTCGAAGAAGCTGTACGTGGCGTGACCAAAGAGATCCGCATTCCGACT
CTGGAAGAGTGTGACGTTTGCCACGGTAGCGGTGCAAAACCAGGTACACAGCCGCAGACT
TGTCCGACCTGTCATGGTTCTGGTCAGGTGCAGATGCGCCAGGGATTCTTCGCTGTACAG
CAGACCTGTCCACACTGTCAGGGCCGCGGTACGCTGATCAAAGATCCGTGCAACAAATGT
CATGGTCATGGTCGTGTTGAGCGCAGCAAAACGCTGTCCGTTAAAATCCCGGCAGGGGTG
GACACTGGAGACCGCATCCGTCTTGCGGGCGAAGGTGAAGCGGGCGAGCATGGCGCACCG
GCAGGCGATCTGTACGTTCAGGTTCAGGTTAAACAGCACCCGATTTTCGAGCGTGAAGGC
AACAACCTGTATTGCGAAGTCCCGATCAACTTCGCTATGGCGGCGCTGGGTGGCGAAATC
GAAGTACCGACCCTTGATGGTCGCGTCAAACTGAAAGTGCCTGGCGAAACCCAGACCGGT
AAGCTATTCCGTATGCGCGGTAAAGGCGTCAAGTCTGTCCGCGGTGGCGCACAGGGTGAT
TTGCTGTGCCGCGTTGTCGTCGAAACACCGGTAGGCCTGAACGAAAGGCAGAAACAGCTG
CTGCAAGAGCTGCAAGAAAGCTTCGGTGGCCCAACCGGCGAGCACAACAGCCCGCGCTCA
AAGAGCTTCTTTGATGGTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAA
Protein Properties
Pfam Domain Function:
Protein Residues:376
Protein Molecular Weight:43517
Protein Theoretical pI:4
PDB File:1MXR
Signaling Regions:
  • None
Transmembrane Regions:
  • None
Protein Sequence:
>Ribonucleoside-diphosphate reductase 1 subunit beta
MAYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDR
IDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHS
RSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNG
KTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEA
LHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGL
NKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVSDNVQVAPQEVEVSSYLVG
QIDSEVDTDDLSNFQL
References
External Links:
ResourceLink
Uniprot ID:P69924
Uniprot Name:RIR2_ECOLI
GenBank Gene ID:AP009048
Genebank Protein ID:21321903
PDB ID:1MXR
Ecogene ID:EG10661
Ecocyc:EG10661
ColiBase:b2235
Kegg Gene:b2235
EchoBASE ID:EB0655
CCDB:RIR2_ECOLI
BacMap:16130170
General Reference:
  • Blattner, F. R., Plunkett, G. 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., Shao, Y. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
  • Carlson, J., Fuchs, J. A., Messing, J. (1984). "Primary structure of the Escherichia coli ribonucleoside diphosphate reductase operon." Proc Natl Acad Sci U S A 81:4294-4297. Pubmed: 6087316
  • Eriksson, M., Uhlin, U., Ramaswamy, S., Ekberg, M., Regnstrom, K., Sjoberg, B. M., Eklund, H. (1997). "Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding." Structure 5:1077-1092. Pubmed: 9309223
  • Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
  • Hogbom, M., Andersson, M. E., Nordlund, P. (2001). "Crystal structures of oxidized dinuclear manganese centres in Mn-substituted class I ribonucleotide reductase from Escherichia coli: carboxylate shifts with implications for O2 activation and radical generation." J Biol Inorg Chem 6:315-323. Pubmed: 11315567
  • Logan, D. T., deMare, F., Persson, B. O., Slaby, A., Sjoberg, B. M., Nordlund, P. (1998). "Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins." Biochemistry 37:10798-10807. Pubmed: 9692970
  • Logan, D. T., Su, X. D., Aberg, A., Regnstrom, K., Hajdu, J., Eklund, H., Nordlund, P. (1996). "Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site." Structure 4:1053-1064. Pubmed: 8805591
  • Nordlund, P., Eklund, H. (1993). "Structure and function of the Escherichia coli ribonucleotide reductase protein R2." J Mol Biol 232:123-164. Pubmed: 8331655
  • Nordlund, P., Sjoberg, B. M., Eklund, H. (1990). "Three-dimensional structure of the free radical protein of ribonucleotide reductase." Nature 345:593-598. Pubmed: 2190093
  • Salowe, S. P., Stubbe, J. (1986). "Cloning, overproduction, and purification of the B2 subunit of ribonucleoside-diphosphate reductase." J Bacteriol 165:363-366. Pubmed: 3511029
  • Tong, W., Burdi, D., Riggs-Gelasco, P., Chen, S., Edmondson, D., Huynh, B. H., Stubbe, J., Han, S., Arvai, A., Tainer, J. (1998). "Characterization of Y122F R2 of Escherichia coli ribonucleotide reductase by time-resolved physical biochemical methods and X-ray crystallography." Biochemistry 37:5840-5848. Pubmed: 9558317
  • Yamamoto, Y., Aiba, H., Baba, T., Hayashi, K., Inada, T., Isono, K., Itoh, T., Kimura, S., Kitagawa, M., Makino, K., Miki, T., Mitsuhashi, N., Mizobuchi, K., Mori, H., Nakade, S., Nakamura, Y., Nashimoto, H., Oshima, T., Oyama, S., Saito, N., Sampei, G., Satoh, Y., Sivasundaram, S., Tagami, H., Horiuchi, T., et, a. l. .. (1997). "Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." DNA Res 4:91-113. Pubmed: 9205837