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Protein

Ribonucleoside-diphosphate reductase 1 subunit alpha

Gene

nrdA

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

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 activityi

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

Enzyme regulationi

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).By similarity

Pathwayi: DNA replication

This protein is involved in the pathway DNA replication, which is part of Genetic information processing.
View all proteins of this organism that are known to be involved in the pathway DNA replication and in Genetic information processing.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei9Allosteric activatorBy similarity1
Binding sitei55Allosteric activatorBy similarity1
Binding sitei91Allosteric activatorBy similarity1
Binding sitei209SubstrateBy similarity1
Sitei225Important for hydrogen atom transferBy similarity1
Sitei232Allosteric effector bindingBy similarity1
Binding sitei253Substrate; via amide nitrogenBy similarity1
Sitei262Allosteric effector bindingBy similarity1
Active sitei437Proton acceptorBy similarity1
Active sitei439Cysteine radical intermediateBy similarity1
Active sitei441Proton acceptorBy similarity1
Sitei462Important for hydrogen atom transferBy similarity1
Sitei730Important for electron transferBy similarity1
Sitei731Important for electron transferBy similarity1
Sitei754Interacts with thioredoxin/glutaredoxinBy similarity1
Sitei759Interacts with thioredoxin/glutaredoxinBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:nrdA
Ordered Locus Names:STM2277
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001872131 – 761Ribonucleoside-diphosphate reductase 1 subunit alphaAdd BLAST761

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi225 ↔ 462Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiP37426.
PRIDEiP37426.

Interactioni

Subunit structurei

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.

Protein-protein interaction databases

STRINGi99287.STM2277.

Structurei

3D structure databases

ProteinModelPortaliP37426.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini5 – 95ATP-conePROSITE-ProRule annotationAdd BLAST91

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni15 – 21Allosteric activator bindingBy similarity7
Regioni224 – 225Substrate bindingBy similarity2
Regioni437 – 441Substrate bindingBy similarity5
Regioni621 – 625Substrate bindingBy similarity5

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105BZH. Bacteria.
COG0209. LUCA.
HOGENOMiHOG000278076.
KOiK00525.
OMAiYELLWQM.
PhylomeDBiP37426.

Family and domain databases

InterProiIPR005144. ATP-cone_dom.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P37426-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNQSLLVTKR DGRTERINLD KIHRVLDWAA EGLNNVSVSQ VELRSHIQFY
60 70 80 90 100
DGIKTSDIHE TIIKAAADLI SRDAPDYQYL AARLAIFHLR KKAFGQFEPP
110 120 130 140 150
ALYHHVVKMV ELGKYDNHLL EDYTEEEFKQ MDSFIVHDRD MTFSYAAVKQ
160 170 180 190 200
LEGKYLVQNR VTGEIYESAQ FLYILVAACL FSNYPRETRL DYVKRFYDAV
210 220 230 240 250
STFKISLPTP IMSGVRTPTR QFSSCVLIEC GDSLDSINAT SSAIVKYVSQ
260 270 280 290 300
RAGIGINAGR IRALGSPIRG GEAFHTGCIP FYKHFQTAVK SCSQGGVRGG
310 320 330 340 350
AATLFYPMWH LEVESLLVLK NNRGVEGNRV RHMDYGVQIN KLMYTRLLKG
360 370 380 390 400
GDITLFSPSD VPGLYDAFFA DQDEFERLYV KYEHDDSIRK QRVKAVELFS
410 420 430 440 450
LMMQERASTG RIYIQNVDHC NTHSPFDPVV APVRQSNLCL EIALPTKPLN
460 470 480 490 500
DVNDENGEIA LCTLSAFNLG AIKTLDELEE LAILAVRALD ALLDYQDYPI
510 520 530 540 550
PAAKRGAMGR RTLGIGVINF AYWLAKNGKR YSDGSANNLT HKTFEAIQYY
560 570 580 590 600
LLKASNELAK EQGACPWFNE TTYAKGILPI DTYKKDLDAI VNEPLHYDWE
610 620 630 640 650
QLRESIKTHG LRNSTLSALM PSETSSQISN ATNGIEPPRG YVSIKASKDG
660 670 680 690 700
ILRQVVPDYE HLKDAYELLW EMPNNDGYLQ LVGIMQKFID QSISANTNYD
710 720 730 740 750
PSRFPSGKVP MQQLLKDLLT AYKFGVKTLY YQNTRDGAED AQDDLAPSIQ
760
DDGCESGACK I
Length:761
Mass (Da):85,736
Last modified:October 1, 1994 - v1
Checksum:i0B3322D847CC58F9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X72948 Genomic DNA. Translation: CAA51452.1.
AE006468 Genomic DNA. Translation: AAL21178.1.
PIRiS32629.
RefSeqiNP_461219.1. NC_003197.1.
WP_001076487.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL21178; AAL21178; STM2277.
GeneIDi1253799.
KEGGistm:STM2277.
PATRICi32383161. VBISalEnt20916_2410.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X72948 Genomic DNA. Translation: CAA51452.1.
AE006468 Genomic DNA. Translation: AAL21178.1.
PIRiS32629.
RefSeqiNP_461219.1. NC_003197.1.
WP_001076487.1. NC_003197.1.

3D structure databases

ProteinModelPortaliP37426.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM2277.

Proteomic databases

PaxDbiP37426.
PRIDEiP37426.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL21178; AAL21178; STM2277.
GeneIDi1253799.
KEGGistm:STM2277.
PATRICi32383161. VBISalEnt20916_2410.

Phylogenomic databases

eggNOGiENOG4105BZH. Bacteria.
COG0209. LUCA.
HOGENOMiHOG000278076.
KOiK00525.
OMAiYELLWQM.
PhylomeDBiP37426.

Enzyme and pathway databases

UniPathwayiUPA00326.

Family and domain databases

InterProiIPR005144. ATP-cone_dom.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRIR1_SALTY
AccessioniPrimary (citable) accession number: P37426
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: November 2, 2016
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.