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P00452 (RIR1_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 157. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribonucleoside-diphosphate reductase 1 subunit alpha

EC=1.17.4.1
Alternative name(s):
Protein B1
Ribonucleoside-diphosphate reductase 1 R1 subunit
Ribonucleotide reductase 1
Gene names
Name:nrdA
Synonyms:dnaF
Ordered Locus Names:b2234, JW2228
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length761 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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.

Catalytic activity

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.

Enzyme regulation

Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding to separate specificity and activation sites on the alpha subunit. The type of nucleotide bound at the specificity site determines substrate preference. It seems probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP reduction and dTTP favors GDP reduction. Stimulated by ATP and inhibited by dATP binding to the activity site. In vitro, its activity is increased by dithiothreitol (DTT) or thioredoxins (non-specific). Ref.12 Ref.13

Pathway

Genetic information processing; DNA replication.

Subunit structure

Tetramer of two alpha (R1) and two beta (R2) subunits. The B1 protein is a dimer of alpha subunits. A radical transfer pathway occurs between 'Tyr-122' of R2 and R1. Ref.12 Ref.13

Post-translational modification

Binding of the substrate occurs primarily when the active-site cysteines are reduced.

Miscellaneous

E.coli produces two separate class I enzymes. This one is the functional enzyme during growth.

Two distinct regulatory sites have been defined: one controls substrate specificity and the other regulates the overall catalytic activity. A substrate-binding catalytic site, located on R1, is formed only in the presence of the second subunit R2.

Sequence similarities

Belongs to the ribonucleoside diphosphate reductase large chain family.

Contains 1 ATP-cone domain.

Sequence caution

The sequence AAA24223.1 differs from that shown. Reason:

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]
Isoform Alpha (identifier: P00452-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform Alpha' (identifier: P00452-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-25: Missing.
     26-26: L → M

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 761761Ribonucleoside-diphosphate reductase 1 subunit alpha
PRO_0000030596

Regions

Domain5 – 9591ATP-cone
Region15 – 217Allosteric activator binding
Region224 – 2252Substrate binding By similarity
Region437 – 4415Substrate binding By similarity
Region621 – 6255Substrate binding

Sites

Active site4371Proton acceptor Ref.8 Ref.9 Ref.12
Active site4391Cysteine radical intermediate Ref.8 Ref.9 Ref.12
Active site4411Proton acceptor Ref.8 Ref.9 Ref.12
Binding site91Allosteric activator
Binding site551Allosteric activator
Binding site911Allosteric activator
Binding site2091Substrate
Binding site2531Substrate; via amide nitrogen By similarity
Site2251Important for hydrogen atom transfer
Site2321Allosteric effector binding
Site2621Allosteric effector binding
Site4621Important for hydrogen atom transfer
Site7301Important for electron transfer
Site7311Important for electron transfer
Site7541Interacts with thioredoxin/glutaredoxin
Site7591Interacts with thioredoxin/glutaredoxin

Amino acid modifications

Modified residue2831N6-acetyllysine Ref.10
Disulfide bond225 ↔ 462Redox-active Ref.12 Ref.13

Natural variations

Alternative sequence1 – 2525Missing in isoform Alpha'.
VSP_018871
Alternative sequence261L → M in isoform Alpha'.
VSP_018872
Natural variant1 – 22Missing in 15% of the chains.
Natural variant11Missing in 30% of the chains.

Experimental info

Mutagenesis4411E → A or Q: Loss of activity. Ref.12
Mutagenesis4411E → D: Decrease in activity. Ref.12
Mutagenesis7301Y → F: Loss of activity. Ref.9
Mutagenesis7311Y → F: Loss of activity. Ref.9

Secondary structure

................................................................................................................................................ 761
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform Alpha [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 7E034F154567C3FC

FASTA76185,775
        10         20         30         40         50         60 
MNQNLLVTKR DGSTERINLD KIHRVLDWAA EGLHNVSISQ VELRSHIQFY DGIKTSDIHE 

        70         80         90        100        110        120 
TIIKAAADLI SRDAPDYQYL AARLAIFHLR KKAYGQFEPP ALYDHVVKMV EMGKYDNHLL 

       130        140        150        160        170        180 
EDYTEEEFKQ MDTFIDHDRD MTFSYAAVKQ LEGKYLVQNR VTGEIYESAQ FLYILVAACL 

       190        200        210        220        230        240 
FSNYPRETRL QYVKRFYDAV STFKISLPTP IMSGVRTPTR QFSSCVLIEC GDSLDSINAT 

       250        260        270        280        290        300 
SSAIVKYVSQ RAGIGINAGR IRALGSPIRG GEAFHTGCIP FYKHFQTAVK SCSQGGVRGG 

       310        320        330        340        350        360 
AATLFYPMWH LEVESLLVLK NNRGVEGNRV RHMDYGVQIN KLMYTRLLKG EDITLFSPSD 

       370        380        390        400        410        420 
VPGLYDAFFA DQEEFERLYT KYEKDDSIRK QRVKAVELFS LMMQERASTG RIYIQNVDHC 

       430        440        450        460        470        480 
NTHSPFDPAI APVRQSNLCL EIALPTKPLN DVNDENGEIA LCTLSAFNLG AINNLDELEE 

       490        500        510        520        530        540 
LAILAVRALD ALLDYQDYPI PAAKRGAMGR RTLGIGVINF AYYLAKHGKR YSDGSANNLT 

       550        560        570        580        590        600 
HKTFEAIQYY LLKASNELAK EQGACPWFNE TTYAKGILPI DTYKKDLDTI ANEPLHYDWE 

       610        620        630        640        650        660 
ALRESIKTHG LRNSTLSALM PSETSSQISN ATNGIEPPRG YVSIKASKDG ILRQVVPDYE 

       670        680        690        700        710        720 
HLHDAYELLW EMPGNDGYLQ LVGIMQKFID QSISANTNYD PSRFPSGKVP MQQLLKDLLT 

       730        740        750        760 
AYKFGVKTLY YQNTRDGAED AQDDLVPSIQ DDGCESGACK I 

« Hide

Isoform Alpha' [UniParc].

Checksum: 498ADEDC2154C084
Show »

FASTA73682,860

References

« Hide 'large scale' references
[1]"Primary structure of the Escherichia coli ribonucleoside diphosphate reductase operon."
Carlson J., Fuchs J.A., Messing J.
Proc. Natl. Acad. Sci. U.S.A. 81:4294-4297(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Nucleotide sequence of the gene coding for the large subunit of ribonucleotide reductase of Escherichia coli. Correction."
Nilsson O., Aaberg A., Lundqvist T., Sjoeberg B.-M.
Nucleic Acids Res. 16:4174-4174(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[3]Sjoeberg B.-M.
Submitted (APR-2004) to the EMBL/GenBank/DDBJ databases
Cited for: SEQUENCE REVISION TO 526-527.
[4]"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."
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. expand/collapse author list , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, 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.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[6]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]"Protein B1 of ribonucleotide reductase. Direct analytical data and comparisons with data indirectly deduced from the nucleotide sequence of the Escherichia coli nrdA gene."
Sjoeberg B.-M., Eriksson S., Joernvall H., Carlquist M., Eklund H.
Eur. J. Biochem. 150:423-427(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: PARTIAL PROTEIN SEQUENCE.
[8]"Evidence for two different classes of redox-active cysteines in ribonucleotide reductase of Escherichia coli."
Aaberg A., Hahne S., Karlsson M., Larsson A., Ormoe M., Aahgren A., Sjoeberg B.-M.
J. Biol. Chem. 264:12249-12252(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: ACTIVE SITES.
[9]"Two conserved tyrosine residues in protein R1 participate in an intermolecular electron transfer in ribonucleotide reductase."
Ekberg M., Sahlin M., Eriksson M., Sjoberg B.M.
J. Biol. Chem. 271:20655-20659(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: ACTIVE SITES, MUTAGENESIS OF TYR-730 AND TYR-731.
[10]"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-283, IDENTIFICATION BY MASS SPECTROMETRY.
Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[11]"Structure of ribonucleotide reductase protein R1."
Uhlin U., Eklund H.
Nature 370:533-539(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[12]"A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase."
Persson A.L., Eriksson M., Katterle B., Potsch S., Sahlin M., Sjoberg B.M.
J. Biol. Chem. 272:31533-31541(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF MUTANTS ALA-441; ASP-441 AND GLN-441, DISULFIDE BOND, SUBUNIT, ACTIVE SITE, ENZYME REGULATION, ENZYME MECHANISM, MUTAGENESIS OF GLU-441.
[13]"Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding."
Eriksson M., Uhlin U., Ramaswamy S., Ekberg M., Regnstroem K., Sjoeberg B.-M., Eklund H.
Structure 5:1077-1092(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEXES WITH ATP; GDP AND TTP, DISULFIDE BOND, SUBUNIT, ENZYME REGULATION.
[14]"Binding specificity and mechanistic insight into glutaredoxin-catalyzed protein disulfide reduction."
Berardi M.J., Bushweller J.H.
J. Mol. Biol. 292:151-161(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 737-761, BINDING SITES.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
K02672 Genomic DNA. Translation: AAA24223.1. Sequence problems.
X06999 Genomic DNA. Translation: CAA30056.2.
U00096 Genomic DNA. Translation: AAC75294.1.
AP009048 Genomic DNA. Translation: BAA16053.1.
PIRRDEC1R. H64993.
RefSeqNP_416737.1. NC_000913.3.
YP_490473.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1QFNNMR-B737-761[»]
1R1RX-ray2.90A/B/C1-761[»]
1RLRX-ray2.50A1-761[»]
2R1RX-ray3.00A/B/C1-761[»]
2X0XX-ray2.30A/B/C1-761[»]
2XAKX-ray2.80A/B/C1-761[»]
2XAPX-ray2.10A/B/C1-761[»]
2XAVX-ray2.80A/B/C1-761[»]
2XAWX-ray3.10A/B/C1-761[»]
2XAXX-ray2.75A/B/C1-761[»]
2XAYX-ray2.65A/B/C1-761[»]
2XAZX-ray2.60A/B/C1-761[»]
2XO4X-ray2.50A/B/C1-761[»]
2XO5X-ray2.70A/B/C1-761[»]
3R1RX-ray3.00A/B/C1-761[»]
3UUSX-ray5.65A/B/C/D1-761[»]
4ERMX-ray3.95A/B/C/D1-761[»]
4ERPX-ray4.45A/B/C/D1-761[»]
4R1RX-ray3.20A/B/C1-761[»]
5R1RX-ray3.10A/B/C1-761[»]
6R1RX-ray3.10A/B/C1-761[»]
7R1RX-ray3.10A/B/C1-761[»]
ProteinModelPortalP00452.
SMRP00452. Positions 4-737.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-584N.
IntActP00452. 9 interactions.
MINTMINT-1233906.
STRING511145.b2234.

Proteomic databases

PaxDbP00452.
PRIDEP00452.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75294; AAC75294; b2234.
BAA16053; BAA16053; BAA16053.
GeneID12933136.
946612.
KEGGecj:Y75_p2196.
eco:b2234.
PATRIC32119827. VBIEscCol129921_2323.

Organism-specific databases

EchoBASEEB0654.
EcoGeneEG10660. nrdA.

Phylogenomic databases

eggNOGCOG0209.
HOGENOMHOG000278076.
KOK00525.
OMAKSHIQFY.
OrthoDBEOG6J48HC.
PhylomeDBP00452.
ProtClustDBPRK09103.

Enzyme and pathway databases

BioCycEcoCyc:NRDA-MONOMER.
ECOL316407:JW2228-MONOMER.
MetaCyc:NRDA-MONOMER.
SABIO-RKP00452.
UniPathwayUPA00326.

Gene expression databases

GenevestigatorP00452.

Family and domain databases

InterProIPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSPR01183. RIBORDTASEM1.
SUPFAMSSF48168. SSF48168. 1 hit.
TIGRFAMsTIGR02506. NrdE_NrdA. 1 hit.
PROSITEPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP00452.
PROP00452.

Entry information

Entry nameRIR1_ECOLI
AccessionPrimary (citable) accession number: P00452
Secondary accession number(s): P78088, P78177
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 157 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene