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Protein

Ribonucleoside-diphosphate reductase large subunit

Gene

rrm1

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

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

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 M1 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 sitei5Allosteric activatorBy similarity1
Binding sitei53Allosteric activatorBy similarity1
Binding sitei88Allosteric activatorBy similarity1
Binding sitei202SubstrateBy similarity1
Sitei218Important for hydrogen atom transferBy similarity1
Sitei226Allosteric effector binding, determines substrate specificityBy similarity1
Binding sitei247Substrate; via amide nitrogenBy similarity1
Sitei256Allosteric effector binding, determines substrate specificityBy similarity1
Active sitei427Proton acceptorBy similarity1
Active sitei429Cysteine radical intermediateBy similarity1
Active sitei431Proton acceptorBy similarity1
Sitei444Important for hydrogen atom transferBy similarity1
Sitei737Important for electron transferBy similarity1
Sitei738Important for electron transferBy similarity1
Sitei789Interacts with thioredoxin/glutaredoxinBy similarity1
Sitei792Interacts 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

UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase large subunit (EC:1.17.4.1)
Alternative name(s):
Ribonucleoside-diphosphate reductase subunit M1
Ribonucleotide reductase large subunit
Ribonucleotide reductase protein R1 class I
Gene namesi
Name:rrm1
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-990415-247. rrm1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001871921 – 794Ribonucleoside-diphosphate reductase large subunitAdd BLAST794

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi218 ↔ 444Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiP79732.
PRIDEiP79732.

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

STRINGi7955.ENSDARP00000010800.

Structurei

3D structure databases

ProteinModelPortaliP79732.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 92ATP-conePROSITE-ProRule annotationAdd BLAST92

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni11 – 17Allosteric activator bindingBy similarity7
Regioni217 – 218Substrate bindingBy similarity2
Regioni285 – 288Allosteric effector binding, determines substrate specificityBy similarity4
Regioni427 – 431Substrate bindingBy similarity5
Regioni603 – 607Substrate bindingBy similarity5

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1112. Eukaryota.
COG0209. LUCA.
HOGENOMiHOG000057035.
HOVERGENiHBG003447.
InParanoidiP79732.
PhylomeDBiP79732.

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.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P79732-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHVIKRDGGQ EGVMFDKITS RIQKLCYGLN SDFVDPTQIT MKVIQGLYSG
60 70 80 90 100
VTTVELDTLA AETAATSTTK HPDYAILAAR IAVSNLHKET KKVFSEVMED
110 120 130 140 150
LYNYVNPLNS RHSPMISKET LDIVLANKDR LNSAIIYDRD FSYNFFGFKT
160 170 180 190 200
LERSYLLKIN GKVAERPQHM LMRVSVGIHK EDIAAAIETY NLLSEKWFTH
210 220 230 240 250
ASPTLFNAGT NRPQLSSCFL LAMKDDSIEG IYDTLKQCAL ISKSAGGIGV
260 270 280 290 300
AVSCIRATGR YIAGTNGNSN GLVPMLRVNN NTARYVDQGG NKRPGAFAMY
310 320 330 340 350
LEPWHFDIFD FLELKKNTGK EEQRARDLFY ALWIPDLFMK RVETNGDWSL
360 370 380 390 400
MCPNDCPGLD ECWGEEFEKL YAKYEQEGRA KRVVKAQQLW YAIIESQTET
410 420 430 440 450
GTPYMLYKDA CNRKSNRQNL GTIKCSNLCT EIVEYTSADE VAVCNLASIA
460 470 480 490 500
LNMYVTSERT FDFQKLASVT KVIVKNLNKI IDINYYPVKE AENSNKRHRP
510 520 530 540 550
IGIGVQGLAD AFILMRFPFE STEAQLLNTQ IFETIYYAAL ESSCELAAEY
560 570 580 590 600
GPYQTYAGCP VSKGILQYDM WEKTPTDLWD WAALKEKIAN DGVRNSLLLA
610 620 630 640 650
PMPTASTAQI LGNNESIEPY TSNIYHRRVL SGEFQIVNPH LLKDLTERGL
660 670 680 690 700
WNEEMKNQII AQNGSIQTIP AIPDDLKELY KTVWEISQKT ILKMAADRGA
710 720 730 740 750
YIDQSQSLNI HIAEPNYGKL TSMHFYGWKQ GLKTGMYYLR TKPGANPIQF
760 770 780 790
TLNKEKLKET QKTTSSEDEE TKERNKAAMV CSLENRHECL MCGS
Length:794
Mass (Da):89,816
Last modified:May 1, 1997 - v1
Checksum:i128355C073B3908C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U57964 mRNA. Translation: AAB37102.1.
UniGeneiDr.33356.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U57964 mRNA. Translation: AAB37102.1.
UniGeneiDr.33356.

3D structure databases

ProteinModelPortaliP79732.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000010800.

Proteomic databases

PaxDbiP79732.
PRIDEiP79732.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Organism-specific databases

ZFINiZDB-GENE-990415-247. rrm1.

Phylogenomic databases

eggNOGiKOG1112. Eukaryota.
COG0209. LUCA.
HOGENOMiHOG000057035.
HOVERGENiHBG003447.
InParanoidiP79732.
PhylomeDBiP79732.

Enzyme and pathway databases

UniPathwayiUPA00326.

Miscellaneous databases

PROiP79732.

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.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRIR1_DANRE
AccessioniPrimary (citable) accession number: P79732
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: May 1, 1997
Last modified: October 5, 2016
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata 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

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.