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P79732

- RIR1_DANRE

UniProt

P79732 - RIR1_DANRE

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Protein

Ribonucleoside-diphosphate reductase large subunit

Gene

rrm1

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - 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

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
Sitei737 – 7371Important for electron transferBy similarity
Sitei738 – 7381Important for electron transferBy similarity
Sitei789 – 7891Interacts with thioredoxin/glutaredoxinBy similarity
Sitei792 – 7921Interacts with thioredoxin/glutaredoxinBy similarity

GO - Molecular functioni

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

GO - Biological processi

  1. deoxyribonucleotide biosynthetic process Source: UniProtKB
  2. DNA replication Source: UniProtKB-UniPathway
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
ProteomesiUP000000437: Unplaced

Organism-specific databases

ZFINiZDB-GENE-990415-247. rrm1.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 794794Ribonucleoside-diphosphate reductase large subunitPRO_0000187192Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP79732.

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

STRINGi7955.ENSDARP00000010800.

Structurei

3D structure databases

ProteinModelPortaliP79732.
SMRiP79732. Positions 15-755.
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
Regioni603 – 6075Substrate bindingBy similarity

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000057035.
HOVERGENiHBG003447.
InParanoidiP79732.
PhylomeDBiP79732.

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.

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:
EMBL
GenBank
DDBJ
Links Updated
U57964 mRNA. Translation: AAB37102.1.
UniGeneiDr.33356.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U57964 mRNA. Translation: AAB37102.1 .
UniGenei Dr.33356.

3D structure databases

ProteinModelPortali P79732.
SMRi P79732. Positions 15-755.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 7955.ENSDARP00000010800.

Proteomic databases

PRIDEi P79732.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Organism-specific databases

ZFINi ZDB-GENE-990415-247. rrm1.

Phylogenomic databases

eggNOGi COG0209.
HOGENOMi HOG000057035.
HOVERGENi HBG003447.
InParanoidi P79732.
PhylomeDBi P79732.

Enzyme and pathway databases

UniPathwayi UPA00326 .

Miscellaneous databases

NextBioi 20807088.
PROi P79732.

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

Publicationsi

  1. "Cloning and sequencing of cDNAs encoding ribonucleotide reductase from zebrafish Danio rerio."
    Mathews C.Z., Sjoeberg B.-M., Karlsson M.
    Mol. Mar. Biol. Biotechnol. 5:284-287(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].

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 29, 2014
This is version 101 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

External Data

Dasty 3