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P37426 (RIR1_SALTY) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 112. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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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
Ordered Locus Names:STM2277
OrganismSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) [Reference proteome] [HAMAP]
Taxonomic identifier99287 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella

Protein attributes

Sequence length761 AA.
Sequence statusComplete.
Protein existenceInferred from homology

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.

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 By similarity.

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.

Miscellaneous

S.typhimurium produces two separate class I enzymes. This one is the functional enzyme during growth.

Sequence similarities

Belongs to the ribonucleoside diphosphate reductase large chain family.

Contains 1 ATP-cone domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 761761Ribonucleoside-diphosphate reductase 1 subunit alpha
PRO_0000187213

Regions

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

Sites

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

Amino acid modifications

Disulfide bond225 ↔ 462Redox-active By similarity

Sequences

Sequence LengthMass (Da)Tools
P37426 [UniParc].

Last modified October 1, 1994. Version 1.
Checksum: 0B3322D847CC58F9

FASTA76185,736
        10         20         30         40         50         60 
MNQSLLVTKR DGRTERINLD KIHRVLDWAA EGLNNVSVSQ VELRSHIQFY DGIKTSDIHE 

        70         80         90        100        110        120 
TIIKAAADLI SRDAPDYQYL AARLAIFHLR KKAFGQFEPP ALYHHVVKMV ELGKYDNHLL 

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

       190        200        210        220        230        240 
FSNYPRETRL DYVKRFYDAV 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 GDITLFSPSD 

       370        380        390        400        410        420 
VPGLYDAFFA DQDEFERLYV KYEHDDSIRK QRVKAVELFS LMMQERASTG RIYIQNVDHC 

       430        440        450        460        470        480 
NTHSPFDPVV APVRQSNLCL EIALPTKPLN DVNDENGEIA LCTLSAFNLG AIKTLDELEE 

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

       550        560        570        580        590        600 
HKTFEAIQYY LLKASNELAK EQGACPWFNE TTYAKGILPI DTYKKDLDAI VNEPLHYDWE 

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

       670        680        690        700        710        720 
HLKDAYELLW EMPNNDGYLQ LVGIMQKFID QSISANTNYD PSRFPSGKVP MQQLLKDLLT 

       730        740        750        760 
AYKFGVKTLY YQNTRDGAED AQDDLAPSIQ DDGCESGACK I 

« 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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: LT2 / SGSC1412 / ATCC 700720.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X72948 Genomic DNA. Translation: CAA51452.1.
AE006468 Genomic DNA. Translation: AAL21178.1.
PIRS32629.
RefSeqNP_461219.1. NC_003197.1.

3D structure databases

ProteinModelPortalP37426.
SMRP37426. Positions 5-737.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING99287.STM2277.

Proteomic databases

PaxDbP37426.
PRIDEP37426.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAL21178; AAL21178; STM2277.
GeneID1253799.
KEGGstm:STM2277.
PATRIC32383161. VBISalEnt20916_2410.

Phylogenomic databases

eggNOGCOG0209.
HOGENOMHOG000278076.
KOK00525.
OMALLWQMPS.
OrthoDBEOG6J48HC.
PhylomeDBP37426.

Enzyme and pathway databases

BioCycSENT99287:GCTI-2292-MONOMER.
UniPathwayUPA00326.

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...

Entry information

Entry nameRIR1_SALTY
AccessionPrimary (citable) accession number: P37426
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: July 9, 2014
This is version 112 of the entry and version 1 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

PATHWAY comments

Index of metabolic and biosynthesis pathways