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E7FHX6

- NDRZ_PYRFU

UniProt

E7FHX6 - NDRZ_PYRFU

Protein

Vitamin B12-dependent ribonucleoside-diphosphate reductase

Gene

rnr

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 32 (01 Oct 2014)
      Sequence version 1 (08 Mar 2011)
      Previous versions | rss
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    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

    5'-deoxyadenosylcobalamine (coenzyme B12).1 Publication

    Kineticsi

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

    Pathwayi

    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

    1. ATP binding Source: UniProtKB-KW
    2. cobalamin binding Source: UniProtKB-KW
    3. endonuclease activity Source: InterPro
    4. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

    GO - Biological processi

    1. DNA replication Source: UniProtKB-UniPathway
    2. intein-mediated protein splicing Source: InterPro

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    ATP-binding, Cobalamin, Cobalt, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-15780.
    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: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. ribonucleoside-diphosphate reductase complex Source: InterPro

    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.

    Structurei

    Secondary structure

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    IPR004042. Intein_endonuc.
    IPR006141. Intein_splice_site.
    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.
    SSF54786. SSF54786. 1 hit.
    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

    MAVEKVMKRD GRIVPFDESR IRWAVQRAMW EVGIRDEKKL DEVVKSIVQR     50
    INELYDGKIP HIENIQDIVE LELMRAGLFE VAKAYILYRK KKAEIREEKK 100
    RILNKKELDE IDKRFSINAL RVLASRYLKK DENGNIVESP RELFERVAIL 150
    AVIPDLLYDE RVFDKNGNYS QDLKRVEYYL EHFEEFDRKY SIGKYKLNKY 200
    HFERMVNLYK ELAEQGKMKV SIDEFLAMLE KGEFNEYEKE INEYFRLMTN 250
    QIFMPNTPAL INSGRPLGML SACFVVPIED DMESIMKAAH DVAMIQKMGG 300
    GCIDGKAKII FENEGEEHLT TMEEMYERYK HLGEFYDEEY NRWGIDVSNV 350
    PIYVKSFDPE SKRVVKGKVN VIWKYELGKD VTKYEIITNK GTKILTSPWH 400
    PFFVLTPDFK IVEKRADELK EGDILIGGMP DGEDYKFIFD YWLAGFIAGD 450
    GCFDKYHSHV KGHEYIYDRL RIYDYRIETF EIINDYLEKT FGRKYSIQKD 500
    RNIYYIDIKA RNITSHYLKL LEGIDNGIPP QILKEGKNAV LSFIAGLFDA 550
    EGHVSNKPGI ELGMVNKRLI EDVTHYLNAL GIKARIREKL RKDGIDYVLH 600
    VEEYSSLLRF YELIGKNLQN EEKREKLEKV LSNHKGGNFG LPLNFNAFKE 650
    WASEYGVEFK TNGSQTIAII NDERISLGQW HTRNRVSKAV LVKMLRKLYE 700
    ATKDEEVKRM LHLIEGLEVV RHITTTNEPR TFYDLTVENY QNYLAGENGM 750
    IFVHNTGLNF SKLRPEGDIV GTTTGAASGP VSFMHLIDAV SDVIKQGGVR 800
    RGANMGILEI WHPDIEKFIH AKEKNIGTNV LSNFNISVGI WEDFWEALKE 850
    GKKYPLINPR TGEVVKEVDP KTLFEELAYM AWAKADPGVI FFDVINRRNV 900
    LKKAKGGPIR ATNPCVVGDT RILTPEGYLK AEEIFSLAKE RGKKEAVAVE 950
    GIAEEGEPYA YSVEILLPGE EKVEYETVHG KVLAVADPVA VPAYVWKVGR 1000
    KKVARVKTKE GYEITATLDH KLMTPEGWKE VGKLKEGDKI LLPRFEVEEE 1050
    FGSESIGEDL AFVLGWFIGD GYLNVNDKRA WFYFNAEKEE EIAVRIRDIL 1100
    VKHFGIKAEL HRYGNQIKLG VRGEAYRWLE NIVKNNEKRI PEIVYRLKPR 1150
    EIAAFLRGLF SADGYVDKDM AIRLTSKSRE LLREVQDLLL LFGILSKIYE 1200
    KPYESEFHYT TKNGEERIYR SKGYYELVIT NYSRKLFAEK IGLEGYKMEK 1250
    LSLKKTKVDQ PIVTVESVEV LGEEIVYDFT VPNYHMYISN GFMSHNCGEE 1300
    PLYEYESCNL ASINLAKFVK YDENGKPYFD WDEYAYVIQK VAKYLDNSID 1350
    VNKFPLPEID YNTKLTRRIG VGMMGLADAL FKLGIPYNSE EGFKFMRKVT 1400
    EYLTFYAYKY SVEAAKKRGT FPLYDKTEYP EGKLPVEGFY HPEIWNLPWD 1450
    KLVEEIKKYG LRNAMVTTCP PTGSVSMIAD TSSGIEPVYA LVYKKSVTVG 1500
    EFYYVDPVFE EELKKRGLYS EELLKKISDN YGSVQGLEEI PEDMQRVFVT 1550
    ALDIHWLDHI IAQASIQMWL TDSASKTINM INEATVEDVK AAYLIARFLG 1600
    CKGVTVYRDG SLSVQVYSVE GEKKKRRFKP KPSEYAKKIL LEIVEKEPWI 1650
    KNFINVDEIL NGKKEQLLFS LRPANESKLK VPGREEEVRP GNIPEEKIRE 1700
    LLGVVYCPVC YEKEGKLVEL KMESGCATCP VCGWSKCVIS 1740
    Length:1,740
    Mass (Da):200,932
    Last modified:March 8, 2011 - v1
    Checksum:i49B27D2C17C3913B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U78098 Genomic DNA. Translation: AAB36947.1.
    AE009950 Genomic DNA. Translation: AAL80564.1.
    PIRiT43215.
    RefSeqiNP_578169.1. NC_003413.1.

    Genome annotation databases

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

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U78098 Genomic DNA. Translation: AAB36947.1 .
    AE009950 Genomic DNA. Translation: AAL80564.1 .
    PIRi T43215.
    RefSeqi NP_578169.1. NC_003413.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DQ3 X-ray 2.10 A 302-755 [» ]
    ProteinModelPortali E7FHX6.
    SMRi E7FHX6. Positions 302-755.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi E7FHX6. 1 interaction.

    Proteomic databases

    PRIDEi E7FHX6.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL80564 ; AAL80564 ; PF0440 .
    GeneIDi 1468281.
    KEGGi pfu:PF0440.

    Phylogenomic databases

    HOGENOMi HOG000229277.
    KOi K00525.
    OMAi ISNGFMS.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci MetaCyc:MONOMER-15780.

    Miscellaneous databases

    EvolutionaryTracei E7FHX6.

    Family and domain databases

    Gene3Di 2.170.16.10. 5 hits.
    3.10.28.10. 3 hits.
    3.30.160.90. 1 hit.
    InterProi IPR005144. ATP-cone.
    IPR028992. Hedgehog/Intein_dom.
    IPR003586. Hint_dom_C.
    IPR003587. Hint_dom_N.
    IPR027434. Homing_endonucl.
    IPR006142. INTEIN.
    IPR004042. Intein_endonuc.
    IPR006141. Intein_splice_site.
    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 ]
    Pfami PF03477. 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 ]
    PRINTSi PR00379. INTEIN.
    SMARTi SM00305. HintC. 2 hits.
    SM00306. HintN. 2 hits.
    [Graphical view ]
    SUPFAMi SSF48168. SSF48168. 1 hit.
    SSF51294. SSF51294. 4 hits.
    SSF54786. SSF54786. 1 hit.
    SSF55608. SSF55608. 4 hits.
    TIGRFAMsi TIGR01443. intein_Cterm. 2 hits.
    TIGR01445. intein_Nterm. 2 hits.
    TIGR02504. NrdJ_Z. 1 hit.
    PROSITEi PS51161. ATP_CONE. 1 hit.
    PS50818. INTEIN_C_TER. 2 hits.
    PS50819. INTEIN_ENDONUCLEASE. 2 hits.
    PS50817. INTEIN_N_TER. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 32 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