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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: 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 sitei20Allosteric activatorBy similarity1
Binding sitei71Allosteric activatorBy similarity1
Binding sitei106Allosteric activatorBy similarity1
Binding sitei220SubstrateBy similarity1
Sitei236Important for hydrogen atom transferBy similarity1
Sitei244Allosteric effector binding, determines substrate specificityBy similarity1
Binding sitei265Substrate; via amide nitrogenBy similarity1
Sitei274Allosteric effector binding, determines substrate specificityBy similarity1
Active sitei446Proton acceptorBy similarity1
Active sitei448Cysteine radical intermediateBy similarity1
Active sitei450Proton acceptorBy similarity1
Sitei463Important for hydrogen atom transferBy similarity1
Sitei765Important for electron transferBy similarity1
Sitei766Important for electron transferBy similarity1
Sitei865Interacts with thioredoxin/glutaredoxinBy similarity1
Sitei868Interacts 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

ReactomeiR-DDI-499943. Synthesis and interconversion of nucleotide di- and triphosphates.
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
Proteomesi
  • UP000002195 Componentsi: Chromosome 4, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0284071. rnrA.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003284981 – 870Ribonucleoside-diphosphate reductase large subunitAdd BLAST870

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi236 ↔ 463Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiQ54Q71.

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.By similarity

Protein-protein interaction databases

STRINGi44689.DDB0230075.

Structurei

3D structure databases

ProteinModelPortaliQ54Q71.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini16 – 110ATP-conePROSITE-ProRule annotationAdd BLAST95

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni26 – 32Allosteric activator bindingBy similarity7
Regioni235 – 236Substrate bindingBy similarity2
Regioni303 – 306Allosteric effector binding, determines substrate specificityBy similarity4
Regioni446 – 450Substrate bindingBy similarity5
Regioni631 – 635Substrate bindingBy similarity5

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi832 – 844Poly-GlnAdd BLAST13

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1112. Eukaryota.
COG0209. LUCA.
InParanoidiQ54Q71.
KOiK10807.
OMAiESAFIQN.
PhylomeDBiQ54Q71.

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.
[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

EnsemblProtistsiEAL65376; EAL65376; 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0230075.

Proteomic databases

PaxDbiQ54Q71.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiEAL65376; EAL65376; DDB_G0284071.
GeneIDi8624396.
KEGGiddi:DDB_G0284071.

Organism-specific databases

dictyBaseiDDB_G0284071. rnrA.

Phylogenomic databases

eggNOGiKOG1112. Eukaryota.
COG0209. LUCA.
InParanoidiQ54Q71.
KOiK10807.
OMAiESAFIQN.
PhylomeDBiQ54Q71.

Enzyme and pathway databases

UniPathwayiUPA00326.
ReactomeiR-DDI-499943. Synthesis and interconversion of nucleotide di- and triphosphates.

Miscellaneous databases

PROiQ54Q71.

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.
[Graphical view]
ProtoNetiSearch...

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: November 2, 2016
This is version 87 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

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.