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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

    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 sitei257SubstrateBy similarity1
    Binding sitei301Substrate; via amide nitrogenBy similarity1
    Active sitei913Proton acceptorBy similarity1
    Active sitei1297Cysteine radical intermediateBy similarity1
    Active sitei1299Proton acceptorBy similarity1

    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

    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
    Proteomesi
    • UP000001013 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004287821 – 301Vitamin B12-dependent ribonucleoside-diphosphate reductase, 1st partSequence analysisAdd BLAST301
    ChainiPRO_0000428783302 – 755Endonuclease PI-PfuISequence analysisAdd BLAST454
    ChainiPRO_0000428784756 – 914Vitamin B12-dependent ribonucleoside-diphosphate reductase, 2nd partSequence analysisAdd BLAST159
    ChainiPRO_0000428785915 – 1296Pfu rnr-2 inteinSequence analysisAdd BLAST382
    ChainiPRO_00004287861297 – 1740Vitamin B12-dependent ribonucleoside-diphosphate reductase, 3rd partSequence analysisAdd BLAST444

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    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 interactor.
    STRINGi186497.PF0440.

    Structurei

    Secondary structure

    11740
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi308 – 315Combined sources8
    Beta strandi317 – 321Combined sources5
    Helixi322 – 329Combined sources8
    Helixi330 – 332Combined sources3
    Beta strandi335 – 337Combined sources3
    Turni338 – 341Combined sources4
    Beta strandi342 – 346Combined sources5
    Beta strandi353 – 358Combined sources6
    Turni359 – 362Combined sources4
    Beta strandi363 – 377Combined sources15
    Beta strandi383 – 388Combined sources6
    Beta strandi393 – 396Combined sources4
    Beta strandi401 – 405Combined sources5
    Beta strandi411 – 415Combined sources5
    Turni416 – 418Combined sources3
    Helixi439 – 450Combined sources12
    Beta strandi451 – 457Combined sources7
    Beta strandi466 – 475Combined sources10
    Helixi477 – 491Combined sources15
    Beta strandi498 – 502Combined sources5
    Beta strandi504 – 508Combined sources5
    Helixi511 – 521Combined sources11
    Helixi524 – 526Combined sources3
    Helixi530 – 533Combined sources4
    Helixi537 – 551Combined sources15
    Beta strandi553 – 555Combined sources3
    Turni556 – 558Combined sources3
    Beta strandi559 – 565Combined sources7
    Helixi567 – 578Combined sources12
    Turni579 – 581Combined sources3
    Beta strandi585 – 590Combined sources6
    Beta strandi592 – 601Combined sources10
    Helixi604 – 613Combined sources10
    Helixi615 – 617Combined sources3
    Helixi621 – 632Combined sources12
    Helixi645 – 653Combined sources9
    Turni654 – 656Combined sources3
    Beta strandi658 – 662Combined sources5
    Beta strandi665 – 670Combined sources6
    Beta strandi673 – 676Combined sources4
    Helixi680 – 683Combined sources4
    Helixi688 – 702Combined sources15
    Helixi705 – 716Combined sources12
    Beta strandi718 – 726Combined sources9
    Beta strandi730 – 737Combined sources8
    Turni738 – 740Combined sources3
    Beta strandi742 – 749Combined sources8
    Beta strandi751 – 754Combined sources4

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiE7FHX6.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini4 – 96ATP-conePROSITE-ProRule annotationAdd BLAST93
    Domaini443 – 582DOD-type homing endonuclease 1PROSITE-ProRule annotationAdd BLAST140
    Domaini1063 – 1194DOD-type homing endonuclease 2PROSITE-ProRule annotationAdd BLAST132

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni272 – 273Substrate bindingBy similarity2
    Regioni913 – 914Substrate bindingBy similarity2
    Regioni1297 – 1299Substrate bindingBy similarity3
    Regioni1471 – 1475Substrate bindingBy similarity5

    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

    eggNOGiarCOG03151. Archaea.
    arCOG03154. Archaea.
    arCOG04276. Archaea.
    COG0209. LUCA.
    COG1372. LUCA.
    HOGENOMiHOG000229277.
    KOiK00525.
    OMAiISNGFMS.

    Family and domain databases

    Gene3Di2.170.16.10. 5 hits.
    3.10.28.10. 4 hits.
    3.30.160.90. 1 hit.
    InterProiIPR005144. ATP-cone_dom.
    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.
    IPR004860. LAGLIDADG_2.
    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. 1 hit.
    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.
    RefSeqiWP_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.
    RefSeqiWP_011011558.1. NC_003413.1.

    3D structure databases

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

    Protein-protein interaction databases

    IntActiE7FHX6. 1 interactor.
    STRINGi186497.PF0440.

    Proteomic databases

    PRIDEiE7FHX6.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Phylogenomic databases

    eggNOGiarCOG03151. Archaea.
    arCOG03154. Archaea.
    arCOG04276. Archaea.
    COG0209. LUCA.
    COG1372. LUCA.
    HOGENOMiHOG000229277.
    KOiK00525.
    OMAiISNGFMS.

    Enzyme and pathway databases

    UniPathwayiUPA00326.
    BRENDAi1.17.4.1. 5243.

    Miscellaneous databases

    EvolutionaryTraceiE7FHX6.

    Family and domain databases

    Gene3Di2.170.16.10. 5 hits.
    3.10.28.10. 4 hits.
    3.30.160.90. 1 hit.
    InterProiIPR005144. ATP-cone_dom.
    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.
    IPR004860. LAGLIDADG_2.
    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. 1 hit.
    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...

    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: November 30, 2016
    This is version 45 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

    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.