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Q54Q71

- RIR1_DICDI

UniProt

Q54Q71 - RIR1_DICDI

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Protein

Ribonucleoside-diphosphate reductase large subunit

Gene
rnrA, DDB_G0284071
Organism
Dictyostelium discoideum (Slime mold)
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 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.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei20 – 201Allosteric activator By similarity
Binding sitei71 – 711Allosteric activator By similarity
Binding sitei106 – 1061Allosteric activator By similarity
Binding sitei220 – 2201Substrate By similarity
Sitei236 – 2361Important for hydrogen atom transfer By similarity
Sitei244 – 2441Allosteric effector binding, determines substrate specificity By similarity
Binding sitei265 – 2651Substrate; via amide nitrogen By similarity
Sitei274 – 2741Allosteric effector binding, determines substrate specificity By similarity
Active sitei446 – 4461Proton acceptor By similarity
Active sitei448 – 4481Cysteine radical intermediate By similarity
Active sitei450 – 4501Proton acceptor By similarity
Sitei463 – 4631Important for hydrogen atom transfer By similarity
Sitei765 – 7651Important for electron transfer By similarity
Sitei766 – 7661Important for electron transfer By similarity
Sitei865 – 8651Interacts with thioredoxin/glutaredoxin By similarity
Sitei868 – 8681Interacts with thioredoxin/glutaredoxin By similarity

GO - Molecular functioni

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

GO - Biological processi

  1. deoxyribonucleoside diphosphate metabolic process Source: dictyBase
  2. deoxyribonucleotide biosynthetic process Source: UniProtKB
  3. DNA replication Source: dictyBase
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: Chromosome 4, UP000002195: Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0284071. rnrA.

Subcellular locationi

Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: dictyBase
  2. ribonucleoside-diphosphate reductase complex 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-active By 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.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini16 – 11095ATP-coneAdd
BLAST

Region

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

Compositional bias

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

Sequence similaritiesi

Contains 1 ATP-cone domain.

Phylogenomic databases

eggNOGiCOG0209.
KOiK10807.
OMAiKECAMIS.
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

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MISNSINVTP NKESKMYVVK RDGTKENVSF DKITSRISFL CEMEPKLNSD    50
IVDPIEVAQK VVSGVFPGVK TTELDNLAAE TAAYMSTRHP DYGILAARIS 100
VSNLHKQTSK SFVETVKKQY EFINPKSNLL APLVSKELYE IVMKHGERLE 150
SVIDYYRDFD YDFFGFKTLE RSYLHRINGK IVERPQHMLM RVSIGIHGED 200
LESAINTYKR LSEKLFTHAT PTLFNAGTPS PQMSSCFLVQ MKEDSIDGIY 250
DTLKQCALIS KSAGGIGIAV HKIRAAQSYI RGTNGTSNGL VPMLRVFNDT 300
ARYVDQGGGK RKGAFAVYLE PWHADVFEFI DLKKNTGKEE MRARDLFYAL 350
WVSDIFMERV EQNGDWALFC PNEAPGLAET HSEEHRALYL KYEATPDLPR 400
RVIKAQELWF AIMESQVETG TPFILYKDAC NAKSNQKNLG TISSSNLCTE 450
IIQYTSPDEI AVCNLASIAL PKFVRQKVGS TDPKEKEFDH QFLFEITKLI 500
TVNLNVIIDR NYYPVAEAKT SNLRHRPIGI GIQGLADVFI KMRMPFDSVA 550
AAKLNVEIAE TIYFAALTAS HELAIRDGTY ESFKGSPASK GILQFDMWNV 600
TPSSRWNWAE LKDNIVNKGG LRNSLLIAPM PTASTSQILG NNECFEPYTS 650
NIYSRRVLAG EFTIVNKQLL EDLMELGIWS PEMKNQIVAA RGSIQSIGGI 700
PDDLKELYKT VWEIRQRTLI DMAADRGAFI DQSQSFNVFI AEPTFAKLTS 750
MHFYSWKKGL KTGMYYLRTR PAADAIQFTV DPIVSQTPKP VENNINSTTP 800
LKTPTKTPNS SNRISTSPTN NLTSPIRFNI TQQQQQQQQQ QQQQNNNEDD 850
LANYDGMTCR REEGCLVCGS 870
Length:870
Mass (Da):98,019
Last modified:May 24, 2005 - v1
Checksum:i41A13B6274074897
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
AAFI02000063 Genomic DNA. Translation: EAL65376.1 .
RefSeqi XP_638726.1. XM_633634.1.

3D structure databases

ProteinModelPortali Q54Q71.
SMRi Q54Q71. Positions 30-812.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 44689.DDB_0230075.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblProtistsi DDB0230075 ; DDB0230075 ; DDB_G0284071 .
GeneIDi 8624396.
KEGGi ddi:DDB_G0284071.

Organism-specific databases

dictyBasei DDB_G0284071. rnrA.

Phylogenomic databases

eggNOGi COG0209.
KOi K10807.
OMAi KECAMIS.
PhylomeDBi Q54Q71.

Enzyme and pathway databases

UniPathwayi UPA00326 .

Miscellaneous databases

PROi Q54Q71.

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.
[Graphical view ]
ProtoNeti Search...

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: September 3, 2014
This is version 71 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