NDRZ_PYRFU
ID NDRZ_PYRFU Reviewed; 1740 AA.
AC E7FHX6; P95484; Q7LX09;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 08-MAR-2011, sequence version 1.
DT 03-AUG-2022, entry version 71.
DE RecName: Full=Vitamin B12-dependent ribonucleoside-diphosphate reductase;
DE Short=B12-dependent RNR;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleotide reductase;
DE Contains:
DE RecName: Full=Endonuclease PI-PfuI;
DE EC=3.1.-.-;
DE AltName: Full=Pfu rnr-1 intein;
DE Contains:
DE RecName: Full=Pfu rnr-2 intein;
DE EC=3.1.-.-;
GN Name=rnr; OrderedLocusNames=PF0440;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-15, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=9012808; DOI=10.1073/pnas.94.2.475;
RA Riera J., Robb F.T., Weiss R., Fontecave M.;
RT "Ribonucleotide reductase in the archaeon Pyrococcus furiosus: a critical
RT enzyme in the evolution of DNA genomes?";
RL Proc. Natl. Acad. Sci. U.S.A. 94:475-478(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 302-755.
RX PubMed=10891276; DOI=10.1006/jmbi.2000.3873;
RA Ichiyanagi K., Ishino Y., Ariyoshi M., Komori K., Morikawa K.;
RT "Crystal structure of an archaeal intein-encoded homing endonuclease PI-
RT PfuI.";
RL J. Mol. Biol. 300:889-901(2000).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides. {ECO:0000269|PubMed:9012808}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-
CC diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-
CC diphosphate; Xref=Rhea:RHEA:23252, Rhea:RHEA-COMP:10698, Rhea:RHEA-
CC COMP:10700, ChEBI:CHEBI:15377, ChEBI:CHEBI:29950, ChEBI:CHEBI:50058,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:73316; EC=1.17.4.1;
CC Evidence={ECO:0000269|PubMed:9012808};
CC -!- COFACTOR:
CC Name=adenosylcob(III)alamin; Xref=ChEBI:CHEBI:18408;
CC Evidence={ECO:0000269|PubMed:9012808};
CC Note=5'-deoxyadenosylcobalamine (coenzyme B12).
CC {ECO:0000269|PubMed:9012808};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=70 uM for CDP (at 80 degrees Celsius)
CC {ECO:0000269|PubMed:9012808};
CC -!- PATHWAY: Genetic information processing; DNA replication.
CC -!- PTM: This protein undergoes a protein self splicing that involves a
CC post-translational excision of the intervening region (intein) followed
CC by peptide ligation. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase class-2
CC family. {ECO:0000305}.
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DR EMBL; U78098; AAB36947.1; -; Genomic_DNA.
DR EMBL; AE009950; AAL80564.1; -; Genomic_DNA.
DR PIR; T43215; T43215.
DR RefSeq; WP_011011558.1; NC_018092.1.
DR PDB; 1DQ3; X-ray; 2.10 A; A=302-755.
DR PDBsum; 1DQ3; -.
DR AlphaFoldDB; E7FHX6; -.
DR SMR; E7FHX6; -.
DR IntAct; E7FHX6; 1.
DR STRING; 186497.PF0440; -.
DR PRIDE; E7FHX6; -.
DR EnsemblBacteria; AAL80564; AAL80564; PF0440.
DR GeneID; 41712240; -.
DR KEGG; pfu:PF0440; -.
DR PATRIC; fig|186497.12.peg.464; -.
DR eggNOG; arCOG03151; Archaea.
DR eggNOG; arCOG03154; Archaea.
DR eggNOG; arCOG04276; Archaea.
DR HOGENOM; CLU_000404_2_3_2; -.
DR OMA; ISNGFMS; -.
DR OrthoDB; 4783at2157; -.
DR PhylomeDB; E7FHX6; -.
DR BioCyc; MetaCyc:MON-15780; -.
DR BRENDA; 1.17.4.1; 5243.
DR UniPathway; UPA00326; -.
DR EvolutionaryTrace; E7FHX6; -.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0031419; F:cobalamin binding; IEA:UniProtKB-KW.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IEA:UniProtKB-EC.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR CDD; cd02888; RNR_II_dimer; 1.
DR Gene3D; 3.10.28.10; -; 3.
DR InterPro; IPR005144; ATP-cone_dom.
DR InterPro; IPR003586; Hint_dom_C.
DR InterPro; IPR003587; Hint_dom_N.
DR InterPro; IPR036844; Hint_dom_sf.
DR InterPro; IPR027434; Homing_endonucl.
DR InterPro; IPR006142; INTEIN.
DR InterPro; IPR030934; Intein_C.
DR InterPro; IPR004042; Intein_endonuc.
DR InterPro; IPR006141; Intein_N.
DR InterPro; IPR004860; LAGLIDADG_2.
DR InterPro; IPR015147; PI-PfuI_intein_endonucl_subdom.
DR InterPro; IPR000788; RNR_lg_C.
DR InterPro; IPR013509; RNR_lsu_N.
DR InterPro; IPR013344; RNR_NrdJ/NrdZ.
DR InterPro; IPR008926; RNR_R1-su_N.
DR InterPro; IPR015146; RNR_stirrup.
DR Pfam; PF03477; ATP-cone; 1.
DR Pfam; PF09062; Endonuc_subdom; 1.
DR Pfam; PF14528; LAGLIDADG_3; 2.
DR Pfam; PF02867; Ribonuc_red_lgC; 1.
DR Pfam; PF00317; Ribonuc_red_lgN; 1.
DR Pfam; PF09061; Stirrup; 1.
DR PRINTS; PR00379; INTEIN.
DR SMART; SM00305; HintC; 2.
DR SMART; SM00306; HintN; 2.
DR SUPFAM; SSF48168; SSF48168; 1.
DR SUPFAM; SSF51294; SSF51294; 2.
DR SUPFAM; SSF55608; SSF55608; 4.
DR TIGRFAMs; TIGR01443; intein_Cterm; 2.
DR TIGRFAMs; TIGR01445; intein_Nterm; 2.
DR TIGRFAMs; TIGR02504; NrdJ_Z; 1.
DR PROSITE; PS51161; ATP_CONE; 1.
DR PROSITE; PS50818; INTEIN_C_TER; 2.
DR PROSITE; PS50819; INTEIN_ENDONUCLEASE; 2.
DR PROSITE; PS50817; INTEIN_N_TER; 2.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Autocatalytic cleavage; Cobalamin; Cobalt;
KW Deoxyribonucleotide synthesis; Direct protein sequencing; Disulfide bond;
KW Endonuclease; Hydrolase; Nuclease; Nucleotide-binding; Oxidoreductase;
KW Protein splicing; Reference proteome; Repeat.
FT CHAIN 1..301
FT /note="Vitamin B12-dependent ribonucleoside-diphosphate
FT reductase, 1st part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000428782"
FT CHAIN 302..755
FT /note="Endonuclease PI-PfuI"
FT /evidence="ECO:0000255"
FT /id="PRO_0000428783"
FT CHAIN 756..914
FT /note="Vitamin B12-dependent ribonucleoside-diphosphate
FT reductase, 2nd part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000428784"
FT CHAIN 915..1296
FT /note="Pfu rnr-2 intein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000428785"
FT CHAIN 1297..1740
FT /note="Vitamin B12-dependent ribonucleoside-diphosphate
FT reductase, 3rd part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000428786"
FT DOMAIN 4..96
FT /note="ATP-cone"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00492"
FT DOMAIN 443..582
FT /note="DOD-type homing endonuclease 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00273"
FT DOMAIN 1063..1194
FT /note="DOD-type homing endonuclease 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00273"
FT ACT_SITE 913
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 1297
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 1299
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 257
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 272..273
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 301
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 913..914
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 1297..1299
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 1471..1475
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT DISULFID 273..1308
FT /note="Redox-active"
FT /evidence="ECO:0000250"
FT STRAND 308..315
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 317..321
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 322..329
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 330..332
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 335..337
FT /evidence="ECO:0007829|PDB:1DQ3"
FT TURN 338..341
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 342..346
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 353..358
FT /evidence="ECO:0007829|PDB:1DQ3"
FT TURN 359..362
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 363..377
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 383..388
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 393..396
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 401..405
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 411..415
FT /evidence="ECO:0007829|PDB:1DQ3"
FT TURN 416..418
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 439..450
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 451..457
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 466..475
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 477..491
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 498..502
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 504..508
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 511..521
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 524..526
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 530..533
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 537..551
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 553..555
FT /evidence="ECO:0007829|PDB:1DQ3"
FT TURN 556..558
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 559..565
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 567..578
FT /evidence="ECO:0007829|PDB:1DQ3"
FT TURN 579..581
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 585..590
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 592..601
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 604..613
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 615..617
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 621..632
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 645..653
FT /evidence="ECO:0007829|PDB:1DQ3"
FT TURN 654..656
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 658..662
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 665..670
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 673..676
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 680..683
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 688..702
FT /evidence="ECO:0007829|PDB:1DQ3"
FT HELIX 705..716
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 718..726
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 730..737
FT /evidence="ECO:0007829|PDB:1DQ3"
FT TURN 738..740
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 742..749
FT /evidence="ECO:0007829|PDB:1DQ3"
FT STRAND 751..754
FT /evidence="ECO:0007829|PDB:1DQ3"
SQ SEQUENCE 1740 AA; 200932 MW; 49B27D2C17C3913B CRC64;
MAVEKVMKRD GRIVPFDESR IRWAVQRAMW EVGIRDEKKL DEVVKSIVQR INELYDGKIP
HIENIQDIVE LELMRAGLFE VAKAYILYRK KKAEIREEKK RILNKKELDE IDKRFSINAL
RVLASRYLKK DENGNIVESP RELFERVAIL AVIPDLLYDE RVFDKNGNYS QDLKRVEYYL
EHFEEFDRKY SIGKYKLNKY HFERMVNLYK ELAEQGKMKV SIDEFLAMLE KGEFNEYEKE
INEYFRLMTN QIFMPNTPAL INSGRPLGML SACFVVPIED DMESIMKAAH DVAMIQKMGG
GCIDGKAKII FENEGEEHLT TMEEMYERYK HLGEFYDEEY NRWGIDVSNV PIYVKSFDPE
SKRVVKGKVN VIWKYELGKD VTKYEIITNK GTKILTSPWH PFFVLTPDFK IVEKRADELK
EGDILIGGMP DGEDYKFIFD YWLAGFIAGD GCFDKYHSHV KGHEYIYDRL RIYDYRIETF
EIINDYLEKT FGRKYSIQKD RNIYYIDIKA RNITSHYLKL LEGIDNGIPP QILKEGKNAV
LSFIAGLFDA EGHVSNKPGI ELGMVNKRLI EDVTHYLNAL GIKARIREKL RKDGIDYVLH
VEEYSSLLRF YELIGKNLQN EEKREKLEKV LSNHKGGNFG LPLNFNAFKE WASEYGVEFK
TNGSQTIAII NDERISLGQW HTRNRVSKAV LVKMLRKLYE ATKDEEVKRM LHLIEGLEVV
RHITTTNEPR TFYDLTVENY QNYLAGENGM IFVHNTGLNF SKLRPEGDIV GTTTGAASGP
VSFMHLIDAV SDVIKQGGVR RGANMGILEI WHPDIEKFIH AKEKNIGTNV LSNFNISVGI
WEDFWEALKE GKKYPLINPR TGEVVKEVDP KTLFEELAYM AWAKADPGVI FFDVINRRNV
LKKAKGGPIR ATNPCVVGDT RILTPEGYLK AEEIFSLAKE RGKKEAVAVE GIAEEGEPYA
YSVEILLPGE EKVEYETVHG KVLAVADPVA VPAYVWKVGR KKVARVKTKE GYEITATLDH
KLMTPEGWKE VGKLKEGDKI LLPRFEVEEE FGSESIGEDL AFVLGWFIGD GYLNVNDKRA
WFYFNAEKEE EIAVRIRDIL VKHFGIKAEL HRYGNQIKLG VRGEAYRWLE NIVKNNEKRI
PEIVYRLKPR EIAAFLRGLF SADGYVDKDM AIRLTSKSRE LLREVQDLLL LFGILSKIYE
KPYESEFHYT TKNGEERIYR SKGYYELVIT NYSRKLFAEK IGLEGYKMEK LSLKKTKVDQ
PIVTVESVEV LGEEIVYDFT VPNYHMYISN GFMSHNCGEE PLYEYESCNL ASINLAKFVK
YDENGKPYFD WDEYAYVIQK VAKYLDNSID VNKFPLPEID YNTKLTRRIG VGMMGLADAL
FKLGIPYNSE EGFKFMRKVT EYLTFYAYKY SVEAAKKRGT FPLYDKTEYP EGKLPVEGFY
HPEIWNLPWD KLVEEIKKYG LRNAMVTTCP PTGSVSMIAD TSSGIEPVYA LVYKKSVTVG
EFYYVDPVFE EELKKRGLYS EELLKKISDN YGSVQGLEEI PEDMQRVFVT ALDIHWLDHI
IAQASIQMWL TDSASKTINM INEATVEDVK AAYLIARFLG CKGVTVYRDG SLSVQVYSVE
GEKKKRRFKP KPSEYAKKIL LEIVEKEPWI KNFINVDEIL NGKKEQLLFS LRPANESKLK
VPGREEEVRP GNIPEEKIRE LLGVVYCPVC YEKEGKLVEL KMESGCATCP VCGWSKCVIS
