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Protein

Ribonucleoside-diphosphate reductase large subunit

Gene

rnrA

Organism
Dictyostelium discoideum (Slime mold)
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 (By similarity).By similarity

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 large 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 sitei20 – 201Allosteric activatorBy similarity
Binding sitei71 – 711Allosteric activatorBy similarity
Binding sitei106 – 1061Allosteric activatorBy similarity
Binding sitei220 – 2201SubstrateBy similarity
Sitei236 – 2361Important for hydrogen atom transferBy similarity
Sitei244 – 2441Allosteric effector binding, determines substrate specificityBy similarity
Binding sitei265 – 2651Substrate; via amide nitrogenBy similarity
Sitei274 – 2741Allosteric effector binding, determines substrate specificityBy similarity
Active sitei446 – 4461Proton acceptorBy similarity
Active sitei448 – 4481Cysteine radical intermediateBy similarity
Active sitei450 – 4501Proton acceptorBy similarity
Sitei463 – 4631Important for hydrogen atom transferBy similarity
Sitei765 – 7651Important for electron transferBy similarity
Sitei766 – 7661Important for electron transferBy similarity
Sitei865 – 8651Interacts with thioredoxin/glutaredoxinBy similarity
Sitei868 – 8681Interacts with thioredoxin/glutaredoxinBy similarity

GO - Molecular functioni

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

GO - Biological processi

  1. deoxyribonucleotide biosynthetic process Source: UniProtKB
  2. 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

UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase large subunit (EC:1.17.4.1)
Alternative name(s):
Ribonucleotide reductase large subunit
Gene namesi
Name:rnrA
ORF Names:DDB_G0284071
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
ProteomesiUP000002195 Componentsi: Chromosome 4, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0284071. rnrA.

Subcellular locationi

  1. Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: dictyBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 870870Ribonucleoside-diphosphate reductase large subunitPRO_0000328498Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi236 ↔ 463Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.By similarity

Protein-protein interaction databases

STRINGi44689.DDB_0230075.

Structurei

3D structure databases

ProteinModelPortaliQ54Q71.
SMRiQ54Q71. Positions 30-812.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini16 – 11095ATP-conePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni26 – 327Allosteric activator bindingBy similarity
Regioni235 – 2362Substrate bindingBy similarity
Regioni303 – 3064Allosteric effector binding, determines substrate specificityBy similarity
Regioni446 – 4505Substrate bindingBy similarity
Regioni631 – 6355Substrate bindingBy similarity

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi832 – 84413Poly-GlnAdd
BLAST

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0209.
InParanoidiQ54Q71.
KOiK10807.
OMAiHRFYDAT.
PhylomeDBiQ54Q71.

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.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q54Q71-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MISNSINVTP NKESKMYVVK RDGTKENVSF DKITSRISFL CEMEPKLNSD
60 70 80 90 100
IVDPIEVAQK VVSGVFPGVK TTELDNLAAE TAAYMSTRHP DYGILAARIS
110 120 130 140 150
VSNLHKQTSK SFVETVKKQY EFINPKSNLL APLVSKELYE IVMKHGERLE
160 170 180 190 200
SVIDYYRDFD YDFFGFKTLE RSYLHRINGK IVERPQHMLM RVSIGIHGED
210 220 230 240 250
LESAINTYKR LSEKLFTHAT PTLFNAGTPS PQMSSCFLVQ MKEDSIDGIY
260 270 280 290 300
DTLKQCALIS KSAGGIGIAV HKIRAAQSYI RGTNGTSNGL VPMLRVFNDT
310 320 330 340 350
ARYVDQGGGK RKGAFAVYLE PWHADVFEFI DLKKNTGKEE MRARDLFYAL
360 370 380 390 400
WVSDIFMERV EQNGDWALFC PNEAPGLAET HSEEHRALYL KYEATPDLPR
410 420 430 440 450
RVIKAQELWF AIMESQVETG TPFILYKDAC NAKSNQKNLG TISSSNLCTE
460 470 480 490 500
IIQYTSPDEI AVCNLASIAL PKFVRQKVGS TDPKEKEFDH QFLFEITKLI
510 520 530 540 550
TVNLNVIIDR NYYPVAEAKT SNLRHRPIGI GIQGLADVFI KMRMPFDSVA
560 570 580 590 600
AAKLNVEIAE TIYFAALTAS HELAIRDGTY ESFKGSPASK GILQFDMWNV
610 620 630 640 650
TPSSRWNWAE LKDNIVNKGG LRNSLLIAPM PTASTSQILG NNECFEPYTS
660 670 680 690 700
NIYSRRVLAG EFTIVNKQLL EDLMELGIWS PEMKNQIVAA RGSIQSIGGI
710 720 730 740 750
PDDLKELYKT VWEIRQRTLI DMAADRGAFI DQSQSFNVFI AEPTFAKLTS
760 770 780 790 800
MHFYSWKKGL KTGMYYLRTR PAADAIQFTV DPIVSQTPKP VENNINSTTP
810 820 830 840 850
LKTPTKTPNS SNRISTSPTN NLTSPIRFNI TQQQQQQQQQ QQQQNNNEDD
860 870
LANYDGMTCR REEGCLVCGS
Length:870
Mass (Da):98,019
Last modified:May 24, 2005 - v1
Checksum:i41A13B6274074897
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000063 Genomic DNA. Translation: EAL65376.1.
RefSeqiXP_638726.1. XM_633634.1.

Genome annotation databases

EnsemblProtistsiDDB0230075; DDB0230075; DDB_G0284071.
GeneIDi8624396.
KEGGiddi:DDB_G0284071.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000063 Genomic DNA. Translation: EAL65376.1.
RefSeqiXP_638726.1. XM_633634.1.

3D structure databases

ProteinModelPortaliQ54Q71.
SMRiQ54Q71. Positions 30-812.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB_0230075.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiDDB0230075; DDB0230075; DDB_G0284071.
GeneIDi8624396.
KEGGiddi:DDB_G0284071.

Organism-specific databases

dictyBaseiDDB_G0284071. rnrA.

Phylogenomic databases

eggNOGiCOG0209.
InParanoidiQ54Q71.
KOiK10807.
OMAiHRFYDAT.
PhylomeDBiQ54Q71.

Enzyme and pathway databases

UniPathwayiUPA00326.

Miscellaneous databases

PROiQ54Q71.

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.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The genome of the social amoeba Dictyostelium discoideum."
    Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
    , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
    Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.

Entry informationi

Entry nameiRIR1_DICDI
AccessioniPrimary (citable) accession number: Q54Q71
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 8, 2008
Last sequence update: May 24, 2005
Last modified: March 4, 2015
This is version 75 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.