Reviewed, UniProtKB/Swiss-Prot Q54Q71 (RIR1_DICDI)

Names and origin

Protein names

Recommended name:
    Ribonucleoside-diphosphate reductase large subunit
    EC=1.17.4.1
Alternative name(s):
    Ribonucleotide reductase large subunit

Gene names

Name:	rnrA
ORF Names:	DDB_G0284071

Organism

Dictyostelium discoideum (Slime mold) [Complete proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	870 AA.
Sequence status	Complete.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides By similarity.
Catalytic activity	2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.
Enzyme regulation	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.
Pathway	Genetic information processing; DNA replication.
Subunit structure	Heterodimer of a large and a small subunit By similarity.
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Belongs to the ribonucleoside diphosphate reductase large chain family. Contains 1 ATP-cone domain.

Ontologies

Keywords
Biological process	DNA replication
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Oxidoreductase
PTM	Disulfide bond
Technical term	Allosteric enzyme Complete proteome
Gene Ontology (GO)
Biological process	DNA replication Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	ribonucleoside-diphosphate reductase complex Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: dictyBase ribonucleoside-diphosphate reductase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 870	870	Ribonucleoside-diphosphate reductase large subunit		PRO_0000328498
Regions
	Domain	16 – 110	95	ATP-cone
	Region	26 – 32	7	Allosteric activator binding By similarity
	Region	235 – 236	2	Substrate binding By similarity
	Region	303 – 306	4	Allosteric effector binding, determines substrate specificity By similarity
	Region	446 – 450	5	Substrate binding By similarity
	Region	631 – 635	5	Substrate binding By similarity
	Compositional bias	832 – 844	13	Poly-Gln
Sites
	Active site	446	1	Proton acceptor By similarity
	Active site	448	1	Cysteine radical intermediate By similarity
	Active site	450	1	Proton acceptor By similarity
	Binding site	20	1	Allosteric activator By similarity
	Binding site	71	1	Allosteric activator By similarity
	Binding site	106	1	Allosteric activator By similarity
	Binding site	220	1	Substrate By similarity
	Binding site	265	1	Substrate; via amide nitrogen By similarity
	Site	236	1	Important for hydrogen atom transfer By similarity
	Site	244	1	Allosteric effector binding, determines substrate specificity By similarity
	Site	274	1	Allosteric effector binding, determines substrate specificity By similarity
	Site	463	1	Important for hydrogen atom transfer By similarity
	Site	765	1	Important for electron transfer By similarity
	Site	766	1	Important for electron transfer By similarity
	Site	865	1	Interacts with thioredoxin/glutaredoxin By similarity
	Site	868	1	Interacts with thioredoxin/glutaredoxin By similarity
Amino acid modifications
	Disulfide bond	236 ↔ 463		Redox-active By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q54Q71-1 [UniParc]. Last modified May 24, 2005. Version 1. Checksum: 41A13B6274074897	FASTA	870	98,019
	10 20 30 40 50 60 MISNSINVTP NKESKMYVVK RDGTKENVSF DKITSRISFL CEMEPKLNSD IVDPIEVAQK 70 80 90 100 110 120 VVSGVFPGVK TTELDNLAAE TAAYMSTRHP DYGILAARIS VSNLHKQTSK SFVETVKKQY 130 140 150 160 170 180 EFINPKSNLL APLVSKELYE IVMKHGERLE SVIDYYRDFD YDFFGFKTLE RSYLHRINGK 190 200 210 220 230 240 IVERPQHMLM RVSIGIHGED LESAINTYKR LSEKLFTHAT PTLFNAGTPS PQMSSCFLVQ 250 260 270 280 290 300 MKEDSIDGIY DTLKQCALIS KSAGGIGIAV HKIRAAQSYI RGTNGTSNGL VPMLRVFNDT 310 320 330 340 350 360 ARYVDQGGGK RKGAFAVYLE PWHADVFEFI DLKKNTGKEE MRARDLFYAL WVSDIFMERV 370 380 390 400 410 420 EQNGDWALFC PNEAPGLAET HSEEHRALYL KYEATPDLPR RVIKAQELWF AIMESQVETG 430 440 450 460 470 480 TPFILYKDAC NAKSNQKNLG TISSSNLCTE IIQYTSPDEI AVCNLASIAL PKFVRQKVGS 490 500 510 520 530 540 TDPKEKEFDH QFLFEITKLI TVNLNVIIDR NYYPVAEAKT SNLRHRPIGI GIQGLADVFI 550 560 570 580 590 600 KMRMPFDSVA AAKLNVEIAE TIYFAALTAS HELAIRDGTY ESFKGSPASK GILQFDMWNV 610 620 630 640 650 660 TPSSRWNWAE LKDNIVNKGG LRNSLLIAPM PTASTSQILG NNECFEPYTS NIYSRRVLAG 670 680 690 700 710 720 EFTIVNKQLL EDLMELGIWS PEMKNQIVAA RGSIQSIGGI PDDLKELYKT VWEIRQRTLI 730 740 750 760 770 780 DMAADRGAFI DQSQSFNVFI AEPTFAKLTS MHFYSWKKGL KTGMYYLRTR PAADAIQFTV 790 800 810 820 830 840 DPIVSQTPKP VENNINSTTP LKTPTKTPNS SNRISTSPTN NLTSPIRFNI TQQQQQQQQQ 850 860 870 QQQQNNNEDD LANYDGMTCR REEGCLVCGS

References

[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: 15875012] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.

+

Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AAFI02000063 Genomic DNA. Translation: EAL65376.1.
RefSeq	XP_638726.1.
3D structure databases
HSSP	HSSP built from PDB template 2CVT based on UniProtKB P21524.
SMR	Q54Q71. Positions 30-812.
ModBase	Search...
Protein-protein interaction databases
STRING	Q54Q71.
Genome annotation databases
GeneID	8624396.
KEGG	ddi:DDB_0230075.
Organism-specific databases
dictyBase	DDB_G0284071. rnrA.
Phylogenomic databases
eggNOG	KOG1112.
HOGENOM	HBG296647.
OMA	SKGVLQY.
PhylomeDB	Q54Q71.
Enzyme and pathway databases
BRENDA	1.17.4.1. 424.
Family and domain databases
InterPro	IPR005144. ATP-cone. IPR013346. NrdE_NrdA. IPR013509. Ribncl_Rdtase_lsu_N. IPR000788. Ribncl_red_lg_C. IPR008926. Ribnucl_Rdtase_R1-su_N. [Graphical view]
PANTHER	PTHR11573. Ribncl_red_lg_C. 1 hit.
Pfam	PF03477. ATP-cone. 1 hit. PF02867. Ribonuc_red_lgC. 1 hit. PF00317. Ribonuc_red_lgN. 1 hit. [Graphical view]
PRINTS	PR01183. RIBORDTASEM1.
TIGRFAMs	TIGR02506. NrdE_NrdA. 1 hit.
PROSITE	PS51161. ATP_CONE. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RIR1_DICDI

Accession

Primary (citable) accession number: Q54Q71

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 8, 2008
Last sequence update:	May 24, 2005
Last modified:	February 9, 2010
This is version 40 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)