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Protein

Vitamin B12-dependent ribonucleoside-diphosphate reductase

Gene

rnr

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 4 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

Cofactori

adenosylcob(III)alamin1 PublicationNote: 5'-deoxyadenosylcobalamine (coenzyme B12).1 Publication

Kineticsi

  1. KM=70 µM for CDP (at 80 degrees Celsius)1 Publication

    Pathway:iDNA 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei257 – 2571SubstrateBy similarity
    Binding sitei301 – 3011Substrate; via amide nitrogenBy similarity
    Active sitei913 – 9131Proton acceptorBy similarity
    Active sitei1297 – 12971Cysteine radical intermediateBy similarity
    Active sitei1299 – 12991Proton acceptorBy similarity

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    ATP-binding, Cobalamin, Cobalt, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-15780.
    BRENDAi1.17.4.1. 5243.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Vitamin B12-dependent ribonucleoside-diphosphate reductase (EC:1.17.4.1)
    Short name:
    B12-dependent RNR
    Alternative name(s):
    Ribonucleotide reductase
    Cleaved into the following 2 chains:
    Alternative name(s):
    Pfu rnr-1 intein
    Gene namesi
    Name:rnr
    Ordered Locus Names:PF0440
    OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
    Taxonomic identifieri186497 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000001013 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 301301Vitamin B12-dependent ribonucleoside-diphosphate reductase, 1st partSequence AnalysisPRO_0000428782Add
    BLAST
    Chaini302 – 755454Endonuclease PI-PfuISequence AnalysisPRO_0000428783Add
    BLAST
    Chaini756 – 914159Vitamin B12-dependent ribonucleoside-diphosphate reductase, 2nd partSequence AnalysisPRO_0000428784Add
    BLAST
    Chaini915 – 1296382Pfu rnr-2 inteinSequence AnalysisPRO_0000428785Add
    BLAST
    Chaini1297 – 1740444Vitamin B12-dependent ribonucleoside-diphosphate reductase, 3rd partSequence AnalysisPRO_0000428786Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi273 ↔ 1308Redox-activeBy similarity

    Post-translational modificationi

    This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.Curated

    Keywords - PTMi

    Autocatalytic cleavage, Disulfide bond, Protein splicing

    Proteomic databases

    PRIDEiE7FHX6.

    Interactioni

    Protein-protein interaction databases

    IntActiE7FHX6. 1 interaction.
    STRINGi186497.PF0440.

    Structurei

    Secondary structure

    1
    1740
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi308 – 3158Combined sources
    Beta strandi317 – 3215Combined sources
    Helixi322 – 3298Combined sources
    Helixi330 – 3323Combined sources
    Beta strandi335 – 3373Combined sources
    Turni338 – 3414Combined sources
    Beta strandi342 – 3465Combined sources
    Beta strandi353 – 3586Combined sources
    Turni359 – 3624Combined sources
    Beta strandi363 – 37715Combined sources
    Beta strandi383 – 3886Combined sources
    Beta strandi393 – 3964Combined sources
    Beta strandi401 – 4055Combined sources
    Beta strandi411 – 4155Combined sources
    Turni416 – 4183Combined sources
    Helixi439 – 45012Combined sources
    Beta strandi451 – 4577Combined sources
    Beta strandi466 – 47510Combined sources
    Helixi477 – 49115Combined sources
    Beta strandi498 – 5025Combined sources
    Beta strandi504 – 5085Combined sources
    Helixi511 – 52111Combined sources
    Helixi524 – 5263Combined sources
    Helixi530 – 5334Combined sources
    Helixi537 – 55115Combined sources
    Beta strandi553 – 5553Combined sources
    Turni556 – 5583Combined sources
    Beta strandi559 – 5657Combined sources
    Helixi567 – 57812Combined sources
    Turni579 – 5813Combined sources
    Beta strandi585 – 5906Combined sources
    Beta strandi592 – 60110Combined sources
    Helixi604 – 61310Combined sources
    Helixi615 – 6173Combined sources
    Helixi621 – 63212Combined sources
    Helixi645 – 6539Combined sources
    Turni654 – 6563Combined sources
    Beta strandi658 – 6625Combined sources
    Beta strandi665 – 6706Combined sources
    Beta strandi673 – 6764Combined sources
    Helixi680 – 6834Combined sources
    Helixi688 – 70215Combined sources
    Helixi705 – 71612Combined sources
    Beta strandi718 – 7269Combined sources
    Beta strandi730 – 7378Combined sources
    Turni738 – 7403Combined sources
    Beta strandi742 – 7498Combined sources
    Beta strandi751 – 7544Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DQ3X-ray2.10A302-755[»]
    ProteinModelPortaliE7FHX6.
    SMRiE7FHX6. Positions 302-755.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiE7FHX6.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini4 – 9693ATP-conePROSITE-ProRule annotationAdd
    BLAST
    Domaini443 – 582140DOD-type homing endonuclease 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini1063 – 1194132DOD-type homing endonuclease 2PROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni272 – 2732Substrate bindingBy similarity
    Regioni913 – 9142Substrate bindingBy similarity
    Regioni1297 – 12993Substrate bindingBy similarity
    Regioni1471 – 14755Substrate bindingBy similarity

    Sequence similaritiesi

    Contains 1 ATP-cone domain.PROSITE-ProRule annotation
    Contains 2 DOD-type homing endonuclease domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    HOGENOMiHOG000229277.
    KOiK00525.
    OMAiISNGFMS.

    Family and domain databases

    Gene3Di2.170.16.10. 5 hits.
    3.10.28.10. 3 hits.
    3.30.160.90. 1 hit.
    InterProiIPR005144. ATP-cone.
    IPR028992. Hedgehog/Intein_dom.
    IPR003586. Hint_dom_C.
    IPR003587. Hint_dom_N.
    IPR027434. Homing_endonucl.
    IPR006142. INTEIN.
    IPR030934. Intein_C.
    IPR004042. Intein_endonuc.
    IPR006141. Intein_N.
    IPR015147. PI-PfuI_intein_endonucl_subdom.
    IPR000788. RNR_lg_C.
    IPR013509. RNR_lsu_N.
    IPR013344. RNR_NrdJ/NrdZ.
    IPR008926. RNR_R1-su_N.
    IPR015146. RNR_stirrup.
    [Graphical view]
    PfamiPF03477. ATP-cone. 1 hit.
    PF09062. Endonuc_subdom. 1 hit.
    PF14528. LAGLIDADG_3. 2 hits.
    PF02867. Ribonuc_red_lgC. 3 hits.
    PF00317. Ribonuc_red_lgN. 1 hit.
    PF09061. Stirrup. 1 hit.
    [Graphical view]
    PRINTSiPR00379. INTEIN.
    SMARTiSM00305. HintC. 2 hits.
    SM00306. HintN. 2 hits.
    [Graphical view]
    SUPFAMiSSF48168. SSF48168. 1 hit.
    SSF51294. SSF51294. 4 hits.
    SSF55608. SSF55608. 4 hits.
    TIGRFAMsiTIGR01443. intein_Cterm. 2 hits.
    TIGR01445. intein_Nterm. 2 hits.
    TIGR02504. NrdJ_Z. 1 hit.
    PROSITEiPS51161. ATP_CONE. 1 hit.
    PS50818. INTEIN_C_TER. 2 hits.
    PS50819. INTEIN_ENDONUCLEASE. 2 hits.
    PS50817. INTEIN_N_TER. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    E7FHX6-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAVEKVMKRD GRIVPFDESR IRWAVQRAMW EVGIRDEKKL DEVVKSIVQR
    60 70 80 90 100
    INELYDGKIP HIENIQDIVE LELMRAGLFE VAKAYILYRK KKAEIREEKK
    110 120 130 140 150
    RILNKKELDE IDKRFSINAL RVLASRYLKK DENGNIVESP RELFERVAIL
    160 170 180 190 200
    AVIPDLLYDE RVFDKNGNYS QDLKRVEYYL EHFEEFDRKY SIGKYKLNKY
    210 220 230 240 250
    HFERMVNLYK ELAEQGKMKV SIDEFLAMLE KGEFNEYEKE INEYFRLMTN
    260 270 280 290 300
    QIFMPNTPAL INSGRPLGML SACFVVPIED DMESIMKAAH DVAMIQKMGG
    310 320 330 340 350
    GCIDGKAKII FENEGEEHLT TMEEMYERYK HLGEFYDEEY NRWGIDVSNV
    360 370 380 390 400
    PIYVKSFDPE SKRVVKGKVN VIWKYELGKD VTKYEIITNK GTKILTSPWH
    410 420 430 440 450
    PFFVLTPDFK IVEKRADELK EGDILIGGMP DGEDYKFIFD YWLAGFIAGD
    460 470 480 490 500
    GCFDKYHSHV KGHEYIYDRL RIYDYRIETF EIINDYLEKT FGRKYSIQKD
    510 520 530 540 550
    RNIYYIDIKA RNITSHYLKL LEGIDNGIPP QILKEGKNAV LSFIAGLFDA
    560 570 580 590 600
    EGHVSNKPGI ELGMVNKRLI EDVTHYLNAL GIKARIREKL RKDGIDYVLH
    610 620 630 640 650
    VEEYSSLLRF YELIGKNLQN EEKREKLEKV LSNHKGGNFG LPLNFNAFKE
    660 670 680 690 700
    WASEYGVEFK TNGSQTIAII NDERISLGQW HTRNRVSKAV LVKMLRKLYE
    710 720 730 740 750
    ATKDEEVKRM LHLIEGLEVV RHITTTNEPR TFYDLTVENY QNYLAGENGM
    760 770 780 790 800
    IFVHNTGLNF SKLRPEGDIV GTTTGAASGP VSFMHLIDAV SDVIKQGGVR
    810 820 830 840 850
    RGANMGILEI WHPDIEKFIH AKEKNIGTNV LSNFNISVGI WEDFWEALKE
    860 870 880 890 900
    GKKYPLINPR TGEVVKEVDP KTLFEELAYM AWAKADPGVI FFDVINRRNV
    910 920 930 940 950
    LKKAKGGPIR ATNPCVVGDT RILTPEGYLK AEEIFSLAKE RGKKEAVAVE
    960 970 980 990 1000
    GIAEEGEPYA YSVEILLPGE EKVEYETVHG KVLAVADPVA VPAYVWKVGR
    1010 1020 1030 1040 1050
    KKVARVKTKE GYEITATLDH KLMTPEGWKE VGKLKEGDKI LLPRFEVEEE
    1060 1070 1080 1090 1100
    FGSESIGEDL AFVLGWFIGD GYLNVNDKRA WFYFNAEKEE EIAVRIRDIL
    1110 1120 1130 1140 1150
    VKHFGIKAEL HRYGNQIKLG VRGEAYRWLE NIVKNNEKRI PEIVYRLKPR
    1160 1170 1180 1190 1200
    EIAAFLRGLF SADGYVDKDM AIRLTSKSRE LLREVQDLLL LFGILSKIYE
    1210 1220 1230 1240 1250
    KPYESEFHYT TKNGEERIYR SKGYYELVIT NYSRKLFAEK IGLEGYKMEK
    1260 1270 1280 1290 1300
    LSLKKTKVDQ PIVTVESVEV LGEEIVYDFT VPNYHMYISN GFMSHNCGEE
    1310 1320 1330 1340 1350
    PLYEYESCNL ASINLAKFVK YDENGKPYFD WDEYAYVIQK VAKYLDNSID
    1360 1370 1380 1390 1400
    VNKFPLPEID YNTKLTRRIG VGMMGLADAL FKLGIPYNSE EGFKFMRKVT
    1410 1420 1430 1440 1450
    EYLTFYAYKY SVEAAKKRGT FPLYDKTEYP EGKLPVEGFY HPEIWNLPWD
    1460 1470 1480 1490 1500
    KLVEEIKKYG LRNAMVTTCP PTGSVSMIAD TSSGIEPVYA LVYKKSVTVG
    1510 1520 1530 1540 1550
    EFYYVDPVFE EELKKRGLYS EELLKKISDN YGSVQGLEEI PEDMQRVFVT
    1560 1570 1580 1590 1600
    ALDIHWLDHI IAQASIQMWL TDSASKTINM INEATVEDVK AAYLIARFLG
    1610 1620 1630 1640 1650
    CKGVTVYRDG SLSVQVYSVE GEKKKRRFKP KPSEYAKKIL LEIVEKEPWI
    1660 1670 1680 1690 1700
    KNFINVDEIL NGKKEQLLFS LRPANESKLK VPGREEEVRP GNIPEEKIRE
    1710 1720 1730 1740
    LLGVVYCPVC YEKEGKLVEL KMESGCATCP VCGWSKCVIS
    Length:1,740
    Mass (Da):200,932
    Last modified:March 8, 2011 - v1
    Checksum:i49B27D2C17C3913B
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U78098 Genomic DNA. Translation: AAB36947.1.
    AE009950 Genomic DNA. Translation: AAL80564.1.
    PIRiT43215.
    RefSeqiNP_578169.1. NC_003413.1.
    WP_011011558.1. NC_003413.1.

    Genome annotation databases

    EnsemblBacteriaiAAL80564; AAL80564; PF0440.
    GeneIDi1468281.
    KEGGipfu:PF0440.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U78098 Genomic DNA. Translation: AAB36947.1.
    AE009950 Genomic DNA. Translation: AAL80564.1.
    PIRiT43215.
    RefSeqiNP_578169.1. NC_003413.1.
    WP_011011558.1. NC_003413.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DQ3X-ray2.10A302-755[»]
    ProteinModelPortaliE7FHX6.
    SMRiE7FHX6. Positions 302-755.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiE7FHX6. 1 interaction.
    STRINGi186497.PF0440.

    Proteomic databases

    PRIDEiE7FHX6.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL80564; AAL80564; PF0440.
    GeneIDi1468281.
    KEGGipfu:PF0440.

    Phylogenomic databases

    HOGENOMiHOG000229277.
    KOiK00525.
    OMAiISNGFMS.

    Enzyme and pathway databases

    UniPathwayiUPA00326.
    BioCyciMetaCyc:MONOMER-15780.
    BRENDAi1.17.4.1. 5243.

    Miscellaneous databases

    EvolutionaryTraceiE7FHX6.

    Family and domain databases

    Gene3Di2.170.16.10. 5 hits.
    3.10.28.10. 3 hits.
    3.30.160.90. 1 hit.
    InterProiIPR005144. ATP-cone.
    IPR028992. Hedgehog/Intein_dom.
    IPR003586. Hint_dom_C.
    IPR003587. Hint_dom_N.
    IPR027434. Homing_endonucl.
    IPR006142. INTEIN.
    IPR030934. Intein_C.
    IPR004042. Intein_endonuc.
    IPR006141. Intein_N.
    IPR015147. PI-PfuI_intein_endonucl_subdom.
    IPR000788. RNR_lg_C.
    IPR013509. RNR_lsu_N.
    IPR013344. RNR_NrdJ/NrdZ.
    IPR008926. RNR_R1-su_N.
    IPR015146. RNR_stirrup.
    [Graphical view]
    PfamiPF03477. ATP-cone. 1 hit.
    PF09062. Endonuc_subdom. 1 hit.
    PF14528. LAGLIDADG_3. 2 hits.
    PF02867. Ribonuc_red_lgC. 3 hits.
    PF00317. Ribonuc_red_lgN. 1 hit.
    PF09061. Stirrup. 1 hit.
    [Graphical view]
    PRINTSiPR00379. INTEIN.
    SMARTiSM00305. HintC. 2 hits.
    SM00306. HintN. 2 hits.
    [Graphical view]
    SUPFAMiSSF48168. SSF48168. 1 hit.
    SSF51294. SSF51294. 4 hits.
    SSF55608. SSF55608. 4 hits.
    TIGRFAMsiTIGR01443. intein_Cterm. 2 hits.
    TIGR01445. intein_Nterm. 2 hits.
    TIGR02504. NrdJ_Z. 1 hit.
    PROSITEiPS51161. ATP_CONE. 1 hit.
    PS50818. INTEIN_C_TER. 2 hits.
    PS50819. INTEIN_ENDONUCLEASE. 2 hits.
    PS50817. INTEIN_N_TER. 2 hits.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Ribonucleotide reductase in the archaeon Pyrococcus furiosus: a critical enzyme in the evolution of DNA genomes?"
      Riera J., Robb F.T., Weiss R., Fontecave M.
      Proc. Natl. Acad. Sci. U.S.A. 94:475-478(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-15, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
    2. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
      Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
      Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
    3. "Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI."
      Ichiyanagi K., Ishino Y., Ariyoshi M., Komori K., Morikawa K.
      J. Mol. Biol. 300:889-901(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 302-755.

    Entry informationi

    Entry nameiNDRZ_PYRFU
    AccessioniPrimary (citable) accession number: E7FHX6
    Secondary accession number(s): P95484, Q7LX09
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 16, 2014
    Last sequence update: March 8, 2011
    Last modified: July 22, 2015
    This is version 39 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Intein-containing proteins
      List of intein-containing protein entries
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.