Ribonucleoside-diphosphate reductase 1 subunit alpha (P00452)

Identification
Name:Ribonucleoside-diphosphate reductase 1 subunit alpha
Synonyms:
  • Protein B1
  • Ribonucleoside-diphosphate reductase 1 R1 subunit
  • Ribonucleotide reductase 1
Gene Name:nrdA
Enzyme Class:
Biological Properties
General Function:Involved in oxidation-reduction process
Specific Function:Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox- active cysteines
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 → 1.0Thumb+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
1.02'-deoxyribonucleoside diphosphate+1.0thioredoxin disulfide+1.0Thumb → 1.0ribonucleoside diphosphate+1.0thioredoxin
1.02'-deoxyribonucleoside diphosphate + 1.0thioredoxin disulfide + 1.0Water → 1.0ribonucleoside diphosphate + 1.0thioredoxin
ReactionCard
Metabolites:
ECMDB IDNameView
ECMDB01341ADPMetaboCard
ECMDB01546CDPMetaboCard
ECMDB21326dADPMetaboCard
ECMDB01245dCDPMetaboCard
ECMDB00960dGDPMetaboCard
ECMDB01000dUDPMetaboCard
ECMDB01201Guanosine diphosphateMetaboCard
ECMDB23749ThioredoxinMetaboCard
ECMDB00295Uridine 5'-diphosphateMetaboCard
ECMDB00494WaterMetaboCard
GO Classification:
Component
macromolecular complex
protein complex
ribonucleoside-diphosphate reductase complex
Function
adenyl nucleotide binding
adenyl ribonucleotide binding
ATP binding
binding
catalytic activity
nucleoside binding
oxidoreductase activity
oxidoreductase activity, acting on CH or CH2 groups
oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor
protein binding
purine nucleoside binding
ribonucleoside-diphosphate reductase activity
Process
cellular macromolecule metabolic process
DNA metabolic process
DNA replication
macromolecule metabolic process
metabolic process
oxidation reduction
Gene Properties
Blattner:b2234
Gene OrientationClockwise
Centisome Percentage:50.50
Left Sequence End2342887
Right Sequence End2345172
Gene Sequence:
>2286 bp
ATGAATCAGAATCTGCTGGTGACAAAGCGCGACGGTAGCACAGAGCGCATCAATCTCGAC
AAAATCCATCGCGTTCTGGATTGGGCGGCAGAAGGACTGCATAACGTTTCGATTTCCCAG
GTCGAGCTGCGCTCCCACATTCAGTTTTATGACGGTATCAAGACCTCTGACATCCACGAA
ACCATTATCAAGGCTGCCGCAGACCTGATCTCCCGTGATGCGCCGGATTATCAGTATCTC
GCCGCGCGCCTGGCGATCTTCCACCTGCGTAAAAAAGCCTACGGCCAGTTTGAGCCGCCT
GCGCTGTACGACCACGTGGTGAAAATGGTCGAGATGGGCAAATACGATAATCATCTGCTG
GAAGACTACACGGAAGAAGAGTTCAAGCAGATGGACACCTTTATCGATCACGACCGTGAT
ATGACCTTCTCTTATGCTGCCGTTAAGCAGCTGGAAGGCAAATATCTGGTACAGAACCGC
GTGACCGGCGAAATCTATGAGAGCGCCCAGTTCCTTTATATTCTAGTTGCCGCGTGCTTG
TTCTCGAACTACCCGCGTGAAACGCGCCTGCAATATGTGAAGCGTTTTTACGACGCGGTT
TCCACATTTAAAATTTCGCTGCCGACGCCAATCATGTCCGGCGTGCGTACCCCGACTCGT
CAGTTCAGCTCCTGCGTACTGATCGAGTGCGGTGACAGCCTGGATTCCATCAACGCCACC
TCCAGCGCGATTGTTAAATACGTTTCCCAGCGTGCCGGGATCGGCATCAACGCCGGGCGT
ATTCGTGCGCTGGGTAGCCCGATTCGCGGTGGTGAAGCGTTCCATACCGGCTGCATTCCG
TTCTACAAACATTTCCAGACAGCGGTGAAATCCTGCTCTCAGGGCGGTGTGCGCGGCGGT
GCGGCAACGCTGTTCTACCCGATGTGGCATCTGGAAGTGGAAAGCCTGCTGGTGTTGAAA
AACAACCGTGGTGTGGAAGGCAACCGCGTGCGTCATATGGACTACGGGGTACAAATCAAC
AAACTGATGTATACCCGTCTGCTGAAAGGTGAAGATATCACCCTGTTCAGCCCGTCCGAC
GTACCGGGGCTGTACGACGCGTTCTTCGCCGATCAGGAAGAGTTTGAACGTCTGTATACC
AAATATGAGAAAGACGACAGCATCCGCAAGCAGCGTGTGAAAGCCGTTGAGCTGTTCTCG
CTGATGATGCAGGAACGTGCGTCTACCGGTCGTATCTATATTCAGAACGTTGACCACTGC
AATACCCATAGCCCGTTTGATCCGGCCATCGCGCCAGTGCGTCAGTCTAACCTGTGCCTG
GAGATAGCCCTGCCGACCAAACCGCTGAACGACGTCAACGACGAGAACGGTGAAATCGCG
CTGTGTACGCTGTCTGCTTTCAACCTGGGCGCAATTAATAACCTGGATGAACTGGAAGAG
CTGGCAATTCTGGCGGTTCGTGCACTTGACGCGCTGCTGGATTATCAGGATTACCCGATC
CCGGCCGCCAAACGTGGAGCGATGGGTCGTCGTACGCTGGGTATTGGTGTGATCAACTTC
GCTTACTACCTGGCGAAGCACGGTAAACGCTACTCCGACGGCAGCGCCAACAACCTGACG
CATAAAACCTTCGAAGCCATTCAGTATTACCTGCTGAAAGCCTCTAATGAGCTGGCGAAA
GAGCAAGGCGCGTGCCCGTGGTTTAACGAAACCACTTACGCGAAAGGGATCCTGCCGATC
GATACCTATAAGAAAGATCTGGATACCATCGCTAATGAGCCGCTGCATTACGACTGGGAA
GCTCTGCGTGAGTCAATCAAAACGCACGGTCTGCGTAACTCCACGCTTTCTGCTCTGATG
CCGTCCGAGACTTCTTCGCAGATCTCTAACGCCACTAACGGTATTGAACCGCCGCGCGGT
TACGTCAGCATCAAAGCGTCGAAAGACGGTATTTTGCGCCAGGTGGTGCCGGACTACGAG
CACCTGCACGACGCCTATGAGCTGCTGTGGGAAATGCCGGGTAACGATGGTTATCTGCAA
CTGGTGGGTATCATGCAGAAATTTATCGATCAGTCGATCTCTGCCAACACCAACTACGAT
CCGTCACGCTTCCCGTCAGGAAAAGTGCCGATGCAGCAGTTGCTGAAAGACCTGCTCACC
GCCTACAAATTCGGGGTCAAAACACTGTATTATCAGAACACCCGTGACGGCGCTGAAGAC
GCACAAGACGATCTGGTGCCGTCAATCCAGGACGATGGCTGCGAAAGCGGCGCATGTAAG
ATCTGA
Protein Properties
Pfam Domain Function:
Protein Residues:761
Protein Molecular Weight:85774
Protein Theoretical pI:6
PDB File:3R1R
Signaling Regions:
  • None
Transmembrane Regions:
  • None
Protein Sequence:
>Ribonucleoside-diphosphate reductase 1 subunit alpha
MNQNLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHE
TIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLL
EDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACL
FSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINAT
SSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGG
AATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSD
VPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHC
NTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEE
LAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLT
HKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWE
ALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYE
HLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLT
AYKFGVKTLYYQNTRDGAEDAQDDLVPSIQDDGCESGACKI
References
External Links:
ResourceLink
Uniprot ID:P00452
Uniprot Name:RIR1_ECOLI
GenBank Gene ID:AP009048
Genebank Protein ID:1799581
PDB ID:3R1R
Ecogene ID:EG10660
Ecocyc:EG10660
ColiBase:b2234
Kegg Gene:b2234
EchoBASE ID:EB0654
CCDB:RIR1_ECOLI
BacMap:16130169
General Reference:
  • Aberg, A., Hahne, S., Karlsson, M., Larsson, A., Ormo, M., Ahgren, A., Sjoberg, B. M. (1989). "Evidence for two different classes of redox-active cysteines in ribonucleotide reductase of Escherichia coli." J Biol Chem 264:12249-12252. Pubmed: 2663852
  • Berardi, M. J., Bushweller, J. H. (1999). "Binding specificity and mechanistic insight into glutaredoxin-catalyzed protein disulfide reduction." J Mol Biol 292:151-161. Pubmed: 10493864
  • 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
  • Ekberg, M., Sahlin, M., Eriksson, M., Sjoberg, B. M. (1996). "Two conserved tyrosine residues in protein R1 participate in an intermolecular electron transfer in ribonucleotide reductase." J Biol Chem 271:20655-20659. Pubmed: 8702814
  • 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
  • Nilsson, O., Aberg, A., Lundqvist, T., Sjoberg, B. M. (1988). "Nucleotide sequence of the gene coding for the large subunit of ribonucleotide reductase of Escherichia coli. Correction." Nucleic Acids Res 16:4174. Pubmed: 3287341
  • Persson, A. L., Eriksson, M., Katterle, B., Potsch, S., Sahlin, M., Sjoberg, B. M. (1997). "A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase." J Biol Chem 272:31533-31541. Pubmed: 9395490
  • Sjoberg, B. M., Eriksson, S., Jornvall, H., Carlquist, M., Eklund, H. (1985). "Protein B1 of ribonucleotide reductase. Direct analytical data and comparisons with data indirectly deduced from the nucleotide sequence of the Escherichia coli nrdA gene." Eur J Biochem 150:423-427. Pubmed: 3894026
  • Uhlin, U., Eklund, H. (1994). "Structure of ribonucleotide reductase protein R1." Nature 370:533-539. Pubmed: 8052308
  • 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
  • Zhang, J., Sprung, R., Pei, J., Tan, X., Kim, S., Zhu, H., Liu, C. F., Grishin, N. V., Zhao, Y. (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8:215-225. Pubmed: 18723842