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Q08698 (RIR3_SALTY) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribonucleoside-diphosphate reductase 2 subunit alpha
EC=1.17.4.1
Alternative name(s):
R1E protein
Ribonucleotide reductase 2
Gene names
Name:nrdE
Ordered Locus Names:STM2807
OrganismSalmonella typhimurium
Taxonomic identifier90371 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella

Protein attributes

Sequence length714 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
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. R1E contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide.

Catalytic activity

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

Enzyme regulation

Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding. 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. Lacks the N-terminal activity site.

Pathway

Genetic information processing; DNA replication.

Subunit structure

Tetramer of two alpha and two beta subunits By similarity.

Sequence similarities

Belongs to the ribonucleoside diphosphate reductase large chain family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.1
Chain2 – 714713Ribonucleoside-diphosphate reductase 2 subunit alpha
PRO_0000187225

Regions

Region177 – 1782Substrate binding By similarity
Region386 – 3905Substrate binding By similarity
Region588 – 5925Substrate binding By similarity

Sites

Active site3861Proton acceptor By similarity
Active site3881Cysteine radical intermediate By similarity
Active site3901Proton acceptor By similarity
Binding site1611Substrate By similarity
Binding site2061Substrate; via amide nitrogen By similarity
Site1781Important for hydrogen atom transfer By similarity
Site1851Allosteric effector binding
Site2151Allosteric effector binding
Site2221Allosteric effector binding
Site4151Important for hydrogen atom transfer By similarity
Site6921Important for electron transfer By similarity
Site6931Important for electron transfer By similarity
Site7091Interacts with thioredoxin/glutaredoxin By similarity
Site7121Interacts with thioredoxin/glutaredoxin By similarity

Amino acid modifications

Disulfide bond178 ↔ 415Redox-active

Secondary structure

1 ......................................................................................................... 714
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q08698 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: B12F79B42B05000D

FASTA71480,587
        10         20         30         40         50         60 
MATTTPERVM QETMDYHALN AMLNLYDKAG HIQFDKDQQA IDAFFATHVR PHSVTFASQH 

        70         80         90        100        110        120 
ERLGTLVREG YYDDAVLARY DRAFVLRLFE HAHASGFRFQ TFLGAWKFYT SYTLKTFDGK 

       130        140        150        160        170        180 
RYLEHFEDRV TMVALTLAQG DETLATQLTD EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL 

       190        200        210        220        230        240 
LRIEDNMESI GRAVNSALQL SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED 

       250        260        270        280        290        300 
AFSYANQLGA RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFRLA 

       310        320        330        340        350        360 
KENAQMALFS PYDIQRRYGK PFGDIAISER YDELIADPHV RKTYINARDF FQTLAEIQFE 

       370        380        390        400        410        420 
SGYPYIMFED TVNRANPIAG RINMSNLCSE ILQVNSASRY DDNLDYTHIG HDISCNLGSL 

       430        440        450        460        470        480 
NIAHVMDSPD IGRTVETAIR GLTAVSDMSH IRSVPSIAAG NAASHAIGLG QMNLHGYLAR 

       490        500        510        520        530        540 
EGIAYGSPEA LDFTNLYFYT ITWHAVHTSM RLARERGKTF AGFAQSRYAS GDYFTQYLQD 

       550        560        570        580        590        600 
DWQPKTAKVR ALFARSGITL PTREMWLKLR DDVMRYGIYN QNLQAVPPTG SISYINHATS 

       610        620        630        640        650        660 
SIHPIVAKIE IRKEGKTGRV YYPAPFMTNE NLDMYQDAYD IGPEKIIDTY AEATRHVDQG 

       670        680        690        700        710 
LSLTLFFPDT ATTRDINKAQ IYAWRKGIKS LYYIRLRQLA LEGTEIEGCV SCAL

« Hide

References

« Hide 'large scale' references
[1]"Cloning and sequencing of the genes from Salmonella typhimurium encoding a new bacterial ribonucleotide reductase."
Jordan A., Gibert I., Barbe J.
J. Bacteriol. 176:3420-3427(1994) [PubMed: 8195103] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-15.
Strain: LT2.
[2]"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2."
McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. expand/collapse author list , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K.
Nature 413:852-856(2001) [PubMed: 11677609] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: LT2 / SGSC1412 / ATCC 700720.
[3]"Structure of the large subunit of class Ib ribonucleotide reductase from Salmonella typhimurium and its complexes with allosteric effectors."
Uppsten M., Farnegardh M., Jordan A., Eliasson R., Eklund H., Uhlin U.
J. Mol. Biol. 330:87-97(2003) [PubMed: 12818204] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEXES WITH ALLOSTERIC EFFECTORS.
[4]"The first holocomplex structure of ribonucleotide reductase gives new insight into its mechanism of action."
Uppsten M., Farnegardh M., Domkin V., Uhlin U.
J. Mol. Biol. 359:365-377(2006) [PubMed: 16631785] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 2-713.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		X73226 Genomic DNA. Translation: CAA51699.1.
AE006468 Genomic DNA. Translation: AAL21692.1.
PIRS34271.
RefSeqNP_461733.1. NC_003197.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1PEMX-ray2.99A1-714[»]
1PEOX-ray3.00A1-714[»]
1PEQX-ray2.80A1-714[»]
1PEUX-ray3.20A1-714[»]
2BQ1X-ray4.00E/F2-713[»]
ProteinModelPortalQ08698.
SMRQ08698. Positions 8-699.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID1254330.
GenomeReviewsGene locus STM2807 in contig AE006468_GR.
KEGGstm:STM2807.
NMPDRfig|99287.1.peg.2710.
PATRIC32384296. VBISalEnt20916_2965.

Phylogenomic databases

HOGENOMHBG348953.
OMARHVDQSI.
ProtClustDBPRK08188.

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-13835.
STYP99287:STM2807-MONOMER.

Family and domain databases

InterProIPR013346. NrdE_NrdA.
IPR013509. Ribncl_Rdtase_lsu_N.
IPR000788. Ribncl_red_lg_C.
IPR008926. Ribnucl_Rdtase_R1-su_N.
IPR013554. Ribonucl_Rdtase_N.
[Graphical view]
KOK00525.
PfamPF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
PF08343. RNR_N. 1 hit.
[Graphical view]
PRINTSPR01183. RIBORDTASEM1.
SUPFAMSSF48168. Ribonucleo_red_N. 1 hit.
TIGRFAMsTIGR02506. NrdE_NrdA. 1 hit.
PROSITEPS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameRIR3_SALTY
AccessionPrimary (citable) accession number: Q08698
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: January 23, 2007
Last modified: January 25, 2012
This is version 100 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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