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Protein

Ribonucleoside-diphosphate reductase large chain

Gene

rnr-1

Organism
Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.1 Publication

Catalytic activityi

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.1 Publication

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 sitei5 – 51Allosteric activatorBy similarity
Binding sitei53 – 531Allosteric activatorBy similarity
Binding sitei88 – 881Allosteric activatorBy similarity
Binding sitei202 – 2021SubstrateBy similarity
Sitei218 – 2181Important for hydrogen atom transferBy similarity
Sitei226 – 2261Allosteric effector binding, determines substrate specificityBy similarity
Binding sitei247 – 2471Substrate; via amide nitrogenBy similarity
Sitei256 – 2561Allosteric effector binding, determines substrate specificityBy similarity
Active sitei427 – 4271Proton acceptorBy similarity
Active sitei429 – 4291Cysteine radical intermediateBy similarity
Active sitei431 – 4311Proton acceptorBy similarity
Sitei444 – 4441Important for hydrogen atom transferBy similarity
Sitei738 – 7381Important for electron transferBy similarity
Sitei739 – 7391Important for electron transferBy similarity
Sitei924 – 9241Interacts with thioredoxin/glutaredoxinBy similarity
Sitei927 – 9271Interacts with thioredoxin/glutaredoxinBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. CDP reductase activity Source: EnsemblFungi
  3. nucleoside diphosphate kinase activity Source: EnsemblFungi
  4. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB

GO - Biological processi

  1. CDP metabolic process Source: EnsemblFungi
  2. dCDP biosynthetic process Source: EnsemblFungi
  3. deoxyribonucleotide biosynthetic process Source: UniProtKB
  4. DNA replication Source: UniProtKB-UniPathway
  5. dTTP biosynthetic process Source: EnsemblFungi
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 chain (EC:1.17.4.1)
Alternative name(s):
Ribonucleotide reductase large subunit
Gene namesi
Name:rnr-1
ORF Names:B2A19.30, NCU03539
OrganismiNeurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Taxonomic identifieri367110 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaPezizomycotinaSordariomycetesSordariomycetidaeSordarialesSordariaceaeNeurospora
ProteomesiUP000001805 Componenti: Chromosome 6, Linkage Group II

Organism-specific databases

EuPathDBiFungiDB:NCU03539.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: EnsemblFungi
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi26 – 261C → Y in un-24; temperature-sensitive mutant. 1 Publication
Mutagenesisi124 – 1241V → I in un-24; temperature-sensitive mutant. 1 Publication
Mutagenesisi125 – 1251M → I in un-24; temperature-sensitive mutant. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 929929Ribonucleoside-diphosphate reductase large chainPRO_0000187202Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi218 ↔ 444Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

BioGridi1974838. 3 interactions.
STRINGi5141.NCU03539.1.

Structurei

3D structure databases

ProteinModelPortaliQ9UW15.
SMRiQ9UW15. Positions 15-769.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 9292ATP-conePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni11 – 177Allosteric activator bindingBy similarity
Regioni217 – 2182Substrate bindingBy similarity
Regioni285 – 2884Allosteric effector binding, determines substrate specificityBy similarity
Regioni427 – 4315Substrate bindingBy similarity
Regioni604 – 6085Substrate bindingBy similarity

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000057035.
InParanoidiQ9UW15.
KOiK10807.
OMAiYELLWQM.
OrthoDBiEOG7C5MHR.

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.

Q9UW15-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYVKKRDGRQ ERVQFDKITA RVSRLCYGLD MNHVDPVAIT QKVISGVYGG
60 70 80 90 100
VTTAQLDDLA AETAAYMTVT HPDYAILAAR IAVSNLHKQT KKQWSLVISE
110 120 130 140 150
LYNYVNPRTG KHSPMIAKDV YECVMRHKDE FDSAIVYDRD FNYQYFGFKT
160 170 180 190 200
LERSYLLKLD GQIAERPQHM IMRVAVGIWG DDVERVIETY NLMSLKTFTH
210 220 230 240 250
ASPTLFNAGT PQPQLSSCFL VDMKEDSIEG IYDTLKTCAM ISKMAGGIGL
260 270 280 290 300
NIHRIRATGS YIAGTNGTSN GIVPMLRVFN NTARYVDQGG NKRPGAFAIY
310 320 330 340 350
LEPWHADVFE FLDLRKNHGK EEVRARDLFL ALWIPDLFMK RVEQNGQWTL
360 370 380 390 400
MCPHECPGLA DVYGDEFEAL YEKYEKEGKG RKTVKAQKLW YAILEAQTET
410 420 430 440 450
GNPFMLYKDA CNRKSNQKNL GTIRSSNLCT EIIEYSAPDE VAVCNLASLA
460 470 480 490 500
LSAFIDYENA SYDFKKLHEV TQVVVRNLNK IIDINHYPVK EAHNSNMRHR
510 520 530 540 550
PIGVGVQGLA DAFLALRMPF DSDAASKLNI QIFETIYHAA LTASCQLAKE
560 570 580 590 600
QGPYATYEGS PVSQGILQYD MWNVTPTNLW DWTALKADIK KYGVRNSLLL
610 620 630 640 650
APMPTASTSQ ILGNNECFEP YTSNIYQRRV LAGEFQVVNP WLLRDLVEMG
660 670 680 690 700
LWSDAMKNRI IAEGGSIQNI QSIPNDIKAL YKTVWEISQR TIVKMAADRG
710 720 730 740 750
AFIDQSQSLN IHMREPTMGK ITSMHFAGWK MGLKTGMYYL RTQAAAQPIQ
760 770 780 790 800
FTVDQEALRA TDDRVAPAHS GLKKRSPPAG TYTSIVLREN TSGPRPYAQT
810 820 830 840 850
GVSGTSTPIG TRDVPTPAST PPPTEVPETL VQSDNRPRPL VSPAKSAGFK
860 870 880 890 900
ADLPEPESPK ALATDPIVKT EDIGSPLLER KEGQNEDVDE DSQERDENIY
910 920
SNAPLSEQQV AACAWNPGAD PSSCEMCSG
Length:929
Mass (Da):103,804
Last modified:April 30, 2003 - v2
Checksum:i68C47E8B21C047B8
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti912 – 9121A → R in AAD49743 (PubMed:10660063).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF171697 Genomic DNA. Translation: AAD49743.1.
AL390092 Genomic DNA. Translation: CAB98233.1.
CM002237 Genomic DNA. Translation: EAA27582.1.
PIRiT43711.
RefSeqiXP_956818.1. XM_951725.3.
UniGeneiNcr.20426.

Genome annotation databases

EnsemblFungiiEFNCRT00000002608; EFNCRP00000002608; EFNCRG00000002605.
GeneIDi3872956.
KEGGincr:NCU03539.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF171697 Genomic DNA. Translation: AAD49743.1.
AL390092 Genomic DNA. Translation: CAB98233.1.
CM002237 Genomic DNA. Translation: EAA27582.1.
PIRiT43711.
RefSeqiXP_956818.1. XM_951725.3.
UniGeneiNcr.20426.

3D structure databases

ProteinModelPortaliQ9UW15.
SMRiQ9UW15. Positions 15-769.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi1974838. 3 interactions.
STRINGi5141.NCU03539.1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiEFNCRT00000002608; EFNCRP00000002608; EFNCRG00000002605.
GeneIDi3872956.
KEGGincr:NCU03539.

Organism-specific databases

EuPathDBiFungiDB:NCU03539.

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000057035.
InParanoidiQ9UW15.
KOiK10807.
OMAiYELLWQM.
OrthoDBiEOG7C5MHR.

Enzyme and pathway databases

UniPathwayiUPA00326.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "An osmotic-remedial, temperature-sensitive mutation in the allosteric activity site of ribonucleotide reductase in Neurospora crassa."
    Smith M.L., Hubbard S.P., Jacobson D.J., Micali O.C., Glass N.L.
    Mol. Gen. Genet. 262:1022-1035(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, ENZYME ACTIVITY, MUTAGENESIS OF CYS-26; VAL-124 AND MET-125.
    Strain: Oak Ridge.
  2. "What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence."
    Mannhaupt G., Montrone C., Haase D., Mewes H.-W., Aign V., Hoheisel J.D., Fartmann B., Nyakatura G., Kempken F., Maier J., Schulte U.
    Nucleic Acids Res. 31:1944-1954(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987.
  3. "The genome sequence of the filamentous fungus Neurospora crassa."
    Galagan J.E., Calvo S.E., Borkovich K.A., Selker E.U., Read N.D., Jaffe D.B., FitzHugh W., Ma L.-J., Smirnov S., Purcell S., Rehman B., Elkins T., Engels R., Wang S., Nielsen C.B., Butler J., Endrizzi M., Qui D.
    , Ianakiev P., Bell-Pedersen D., Nelson M.A., Werner-Washburne M., Selitrennikoff C.P., Kinsey J.A., Braun E.L., Zelter A., Schulte U., Kothe G.O., Jedd G., Mewes H.-W., Staben C., Marcotte E., Greenberg D., Roy A., Foley K., Naylor J., Stange-Thomann N., Barrett R., Gnerre S., Kamal M., Kamvysselis M., Mauceli E.W., Bielke C., Rudd S., Frishman D., Krystofova S., Rasmussen C., Metzenberg R.L., Perkins D.D., Kroken S., Cogoni C., Macino G., Catcheside D.E.A., Li W., Pratt R.J., Osmani S.A., DeSouza C.P.C., Glass N.L., Orbach M.J., Berglund J.A., Voelker R., Yarden O., Plamann M., Seiler S., Dunlap J.C., Radford A., Aramayo R., Natvig D.O., Alex L.A., Mannhaupt G., Ebbole D.J., Freitag M., Paulsen I., Sachs M.S., Lander E.S., Nusbaum C., Birren B.W.
    Nature 422:859-868(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987.

Entry informationi

Entry nameiRIR1_NEUCR
AccessioniPrimary (citable) accession number: Q9UW15
Secondary accession number(s): Q7RXZ9, Q9P3G2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 30, 2003
Last sequence update: April 30, 2003
Last modified: April 29, 2015
This is version 114 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

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.