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P37426

- RIR1_SALTY

UniProt

P37426 - RIR1_SALTY

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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: 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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei9 – 91Allosteric activatorBy similarity
Binding sitei55 – 551Allosteric activatorBy similarity
Binding sitei91 – 911Allosteric activatorBy similarity
Binding sitei209 – 2091SubstrateBy similarity
Sitei225 – 2251Important for hydrogen atom transferBy similarity
Sitei232 – 2321Allosteric effector bindingBy similarity
Binding sitei253 – 2531Substrate; via amide nitrogenBy similarity
Sitei262 – 2621Allosteric effector bindingBy similarity
Active sitei437 – 4371Proton acceptorBy similarity
Active sitei439 – 4391Cysteine radical intermediateBy similarity
Active sitei441 – 4411Proton acceptorBy similarity
Sitei462 – 4621Important for hydrogen atom transferBy similarity
Sitei730 – 7301Important for electron transferBy similarity
Sitei731 – 7311Important for electron transferBy similarity
Sitei754 – 7541Interacts with thioredoxin/glutaredoxinBy similarity
Sitei759 – 7591Interacts with thioredoxin/glutaredoxinBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

GO - Biological processi

  1. DNA replication Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciSENT99287:GCTI-2292-MONOMER.
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000001014: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 761761Ribonucleoside-diphosphate reductase 1 subunit alphaPRO_0000187213Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
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.
SMRiP37426. Positions 5-737.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini5 – 9591ATP-conePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni15 – 217Allosteric activator bindingBy similarity
Regioni224 – 2252Substrate bindingBy similarity
Regioni437 – 4415Substrate bindingBy similarity
Regioni621 – 6255Substrate bindingBy similarity

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000278076.
KOiK00525.
OMAiLLWQMPS.
OrthoDBiEOG6J48HC.
PhylomeDBiP37426.

Family and domain databases

InterProiIPR005144. ATP-cone.
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:
EMBL
GenBank
DDBJ
Links Updated
X72948 Genomic DNA. Translation: CAA51452.1.
AE006468 Genomic DNA. Translation: AAL21178.1.
PIRiS32629.
RefSeqiNP_461219.1. NC_003197.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X72948 Genomic DNA. Translation: CAA51452.1 .
AE006468 Genomic DNA. Translation: AAL21178.1 .
PIRi S32629.
RefSeqi NP_461219.1. NC_003197.1.

3D structure databases

ProteinModelPortali P37426.
SMRi P37426. Positions 5-737.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 99287.STM2277.

Proteomic databases

PaxDbi P37426.
PRIDEi P37426.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL21178 ; AAL21178 ; STM2277 .
GeneIDi 1253799.
KEGGi stm:STM2277.
PATRICi 32383161. VBISalEnt20916_2410.

Phylogenomic databases

eggNOGi COG0209.
HOGENOMi HOG000278076.
KOi K00525.
OMAi LLWQMPS.
OrthoDBi EOG6J48HC.
PhylomeDBi P37426.

Enzyme and pathway databases

UniPathwayi UPA00326 .
BioCyci SENT99287:GCTI-2292-MONOMER.

Family and domain databases

InterProi IPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view ]
Pfami PF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view ]
PRINTSi PR01183. RIBORDTASEM1.
SUPFAMi SSF48168. SSF48168. 1 hit.
TIGRFAMsi TIGR02506. NrdE_NrdA. 1 hit.
PROSITEi PS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LT2 / SGSC1412 / ATCC 700720.

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: October 29, 2014
This is version 114 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

External Data

Dasty 3