L_DUGBA
ID L_DUGBA Reviewed; 4036 AA.
AC Q66431;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=RNA-directed RNA polymerase L;
DE Short=Protein L;
DE AltName: Full=Large structural protein;
DE AltName: Full=Replicase;
DE AltName: Full=Transcriptase;
DE Includes:
DE RecName: Full=Ubiquitinyl hydrolase;
DE EC=3.4.19.12 {ECO:0000269|PubMed:23345508};
DE EC=3.4.22.- {ECO:0000269|PubMed:23345508};
DE Includes:
DE RecName: Full=cap-snatching endonuclease;
DE EC=3.1.-.- {ECO:0000250|UniProtKB:Q6GWS6};
DE Includes:
DE RecName: Full=RNA-directed RNA polymerase;
DE EC=2.7.7.48;
GN Name=L;
OS Dugbe virus (isolate ArD44313) (DUGV).
OC Viruses; Riboviria; Orthornavirae; Negarnaviricota; Polyploviricotina;
OC Ellioviricetes; Bunyavirales; Nairoviridae; Orthonairovirus.
OX NCBI_TaxID=766194;
OH NCBI_TaxID=34610; Amblyomma variegatum (Tropical bont tick).
OH NCBI_TaxID=9606; Homo sapiens (Human).
OH NCBI_TaxID=72862; Hyalomma rufipes (Tick) (Hyalomma marginatum rufipes).
OH NCBI_TaxID=72855; Hyalomma truncatum.
OH NCBI_TaxID=34630; Rhipicephalus.
OH NCBI_TaxID=34611; Rhipicephalus annulatus.
OH NCBI_TaxID=60189; Rhipicephalus decoloratus (African blue tick) (Boophilus decoloratus).
OH NCBI_TaxID=136141; Rhipicephalus geigyi.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=8760425; DOI=10.1099/0022-1317-77-8-1775;
RA Marriott A.C., Nuttall P.A.;
RT "Large RNA segment of Dugbe nairovirus encodes the putative RNA
RT polymerase.";
RL J. Gen. Virol. 77:1775-1780(1996).
RN [2]
RP REVIEW.
RX PubMed=28418734; DOI=10.1080/1040841x.2017.1307805;
RA Amroun A., Priet S., de Lamballerie X., Querat G.;
RT "Bunyaviridae RdRps: structure, motifs, and RNA synthesis machinery.";
RL Crit. Rev. Microbiol. 43:753-778(2017).
RN [3] {ECO:0007744|PDB:4HXD}
RP X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF 2-169 IN COMPLEX WITH UBIQUITIN,
RP CATALYTIC ACTIVITY, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION
RP WITH HOST UBIQUITIN, AND MUTAGENESIS OF GLU-10; GLY-101 AND THR-128.
RX PubMed=23345508; DOI=10.1128/jvi.03252-12;
RA Capodagli G.C., Deaton M.K., Baker E.A., Lumpkin R.J., Pegan S.D.;
RT "Diversity of ubiquitin and ISG15 specificity among nairoviruses' viral
RT ovarian tumor domain proteases.";
RL J. Virol. 87:3815-3827(2013).
CC -!- FUNCTION: Displays RNA-directed RNA polymerase, deubiquitinating and
CC deISGylase activities (PubMed:23345508). RNA-dependent RNA polymerase
CC is responsible for replication and transcription of the viral RNA
CC genome (By similarity). During transcription, synthesizes subgenomic
CC RNAs and assures their capping by a cap-snatching mechanism, which
CC involves the endonuclease activity cleaving the host capped pre-mRNAs.
CC These short capped RNAs are then used as primers for viral
CC transcription (By similarity). The deubiquitinating and deISGylating
CC activities specifically cleaves poly-ubiquitinated conjugates and ISG15
CC from RIG-I, interfering with antiviral signaling pathways mediated by
CC NF-kappaB and IRF signalings (By similarity). Favors K48 poly-Ub
CC linkages (PubMed:23345508). {ECO:0000250|UniProtKB:Q6GWS6,
CC ECO:0000250|UniProtKB:Q6TQR6, ECO:0000269|PubMed:23345508}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC residue protein attached to proteins as an intracellular targeting
CC signal).; EC=3.4.19.12; Evidence={ECO:0000269|PubMed:23345508};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU00539};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=35.7 uM for Ub-AMC {ECO:0000269|PubMed:23345508};
CC KM=5.21 uM for ISG15-AMC {ECO:0000269|PubMed:23345508};
CC -!- SUBUNIT: Interacts (via N-terminus) with host ISG15 (via C-terminus);
CC the deISGylase activity of the viral protein interferes with antiviral
CC signaling pathways mediated by NF-kappaB and IRF signalings (By
CC similarity). Interacts with host ubiquitin (PubMed:23345508).
CC {ECO:0000250|UniProtKB:Q6TQR6, ECO:0000269|PubMed:23345508}.
CC -!- DOMAIN: The viral OTU domain (vOTU) and its N-terminal extension is
CC responsible for ubiquitin and ISG15 binding and for the
CC deubiquitination and deISGylation activities.
CC {ECO:0000250|UniProtKB:Q6TQR6}.
CC -!- MISCELLANEOUS: Classified as His(+) endonuclease since it has a
CC histidine upstream of the active site that coordinates the first
CC cation. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the Bunyavirales RNA polymerase family.
CC {ECO:0000305}.
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DR EMBL; U15018; AAB18834.1; -; Genomic_RNA.
DR PDB; 4HXD; X-ray; 2.85 A; B/D=2-169.
DR PDBsum; 4HXD; -.
DR SMR; Q66431; -.
DR MEROPS; C87.001; -.
DR PRIDE; Q66431; -.
DR Proteomes; UP000000278; Genome.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IEA:UniProtKB-EC.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0039648; P:modulation by virus of host protein ubiquitination; IEA:UniProtKB-KW.
DR GO; GO:0039689; P:negative stranded viral RNA replication; ISS:UniProtKB.
DR GO; GO:0039696; P:RNA-templated viral transcription; ISS:UniProtKB.
DR GO; GO:0039579; P:suppression by virus of host ISG15-protein conjugation; IEA:UniProtKB-KW.
DR GO; GO:0039502; P:suppression by virus of host type I interferon-mediated signaling pathway; IEA:UniProtKB-KW.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR InterPro; IPR003323; OTU_dom.
DR InterPro; IPR007099; RNA-dir_pol_NSvirus.
DR InterPro; IPR007322; RNA_pol_bunyavir.
DR Pfam; PF04196; Bunya_RdRp; 1.
DR Pfam; PF02338; OTU; 1.
DR PROSITE; PS50802; OTU; 1.
DR PROSITE; PS50525; RDRP_SSRNA_NEG_SEG; 1.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Host-virus interaction; Hydrolase;
KW Inhibition of host innate immune response by virus;
KW Inhibition of host interferon signaling pathway by virus;
KW Inhibition of host ISG15 by virus; Magnesium; Metal-binding;
KW Modulation of host ubiquitin pathway by viral deubiquitinase;
KW Modulation of host ubiquitin pathway by virus; Nucleotide-binding;
KW Nucleotidyltransferase; Reference proteome; RNA-directed RNA polymerase;
KW Transferase; Viral immunoevasion; Viral RNA replication.
FT CHAIN 1..4036
FT /note="RNA-directed RNA polymerase L"
FT /id="PRO_0000222026"
FT DOMAIN 29..158
FT /note="OTU"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00139"
FT DOMAIN 2424..2639
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT REGION 1..28
FT /note="Essential for the vOTU enzymatic activity"
FT /evidence="ECO:0000250|UniProtKB:Q6GWS6"
FT REGION 624..805
FT /note="Endonuclease"
FT /evidence="ECO:0000250|UniProtKB:Q6GWS6"
FT REGION 779..879
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2800..2833
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 4008..4036
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 793..812
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 828..846
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 847..870
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 4016..4036
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 40
FT /note="For ubiquitin thioesterase activity"
FT /evidence="ECO:0000250|UniProtKB:Q6TQR6"
FT ACT_SITE 151
FT /note="For ubiquitin thioesterase activity"
FT /evidence="ECO:0000250|UniProtKB:Q6TQR6"
FT ACT_SITE 153
FT /note="For ubiquitin thioesterase activity"
FT /evidence="ECO:0000250|UniProtKB:Q6TQR6"
FT ACT_SITE 733
FT /note="For endonuclease activity"
FT /evidence="ECO:0000250|UniProtKB:I0DF35"
FT BINDING 631
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q6GWS6"
FT BINDING 692
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q6GWS6"
FT BINDING 692
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q6GWS6"
FT BINDING 717
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q6GWS6"
FT BINDING 2606
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic; for RdRp activity"
FT /evidence="ECO:0000250|UniProtKB:I0DF35"
FT MUTAGEN 10
FT /note="E->T: 75% loss of debubiquitination activity and 60%
FT loss of deISGylation activity."
FT /evidence="ECO:0000269|PubMed:23345508"
FT MUTAGEN 101
FT /note="G->S: More than 90% loss of deISGylation and
FT debubiquitination activities."
FT /evidence="ECO:0000269|PubMed:23345508"
FT MUTAGEN 128
FT /note="T->E: 110% increase in debubiquitination activity
FT and almost 2,000% increase in deISGylation activity."
FT /evidence="ECO:0000269|PubMed:23345508"
FT HELIX 3..6
FT /evidence="ECO:0007829|PDB:4HXD"
FT STRAND 10..13
FT /evidence="ECO:0007829|PDB:4HXD"
FT STRAND 16..19
FT /evidence="ECO:0007829|PDB:4HXD"
FT HELIX 25..28
FT /evidence="ECO:0007829|PDB:4HXD"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:4HXD"
FT STRAND 36..38
FT /evidence="ECO:0007829|PDB:4HXD"
FT HELIX 40..49
FT /evidence="ECO:0007829|PDB:4HXD"
FT STRAND 50..52
FT /evidence="ECO:0007829|PDB:4HXD"
FT TURN 55..57
FT /evidence="ECO:0007829|PDB:4HXD"
FT HELIX 58..72
FT /evidence="ECO:0007829|PDB:4HXD"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:4HXD"
FT HELIX 77..80
FT /evidence="ECO:0007829|PDB:4HXD"
FT HELIX 86..93
FT /evidence="ECO:0007829|PDB:4HXD"
FT HELIX 102..111
FT /evidence="ECO:0007829|PDB:4HXD"
FT STRAND 116..121
FT /evidence="ECO:0007829|PDB:4HXD"
FT STRAND 125..135
FT /evidence="ECO:0007829|PDB:4HXD"
FT STRAND 141..146
FT /evidence="ECO:0007829|PDB:4HXD"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:4HXD"
FT STRAND 152..157
FT /evidence="ECO:0007829|PDB:4HXD"
SQ SEQUENCE 4036 AA; 459392 MW; E2EDF0B4358E31BD CRC64;
MDFLDSLIWE RVVDEQYITN PTFCVSDYFE VIRQPGDGNC FYHSIAELFF DVKTPSSFRK
VKEHLQLAAE VYYDTEPEAV GTGISKDEYI KVAMKDNEWG GSLEASMLSK HLQTTIILWV
VNSTEQVTAA IKFGPGRVST ALNLMHVGRT HFDALRIIEQ LENNQPQDRN RLDIADRIAA
AEVYVRQSIE DNLQEDEFFD YAREDEISED VSAPGGSREA TELKKKAILL NKTVKRGENI
PIRVGRVLDC LFSCKIAVSL DEGLLYLRPE TRESEATSIS LRQLGHKLLT RDRHIKMEYA
RSKLYVTRDL IDHLDIGGLL RSSFPGLGLE RYIQLLHSEL VLDLVTVVLA VLLSTFLYGS
NNKNKKQFIT NCLLNTKLSG KRVFKALSKL TGQMLYRTPK RAVSIVSQEL YGKLMLKVKN
NLEGMGPISM LALRNLNFDN MQLQDYLEML SEMSKIDNSD VEYTHREISD LHTLVERLSK
LQKSQDVNEL KLWFKEEVLT KRSQRSVGNA FEFLINDYFK KKDIMKFVST SGKASSTGNI
GNVLSYAHNL YLSKESLRMT SEDVTQLLIE IRKLHKLQGD LSIEPVAIIC DKLEDQFRKL
FRELPEECSS ECQTLFNDIR NSPSHSVAWK HALRLKGTAY EGMFAKQYGW SYISEDIKPS
LTMIVQTLFP ESFEAFLDRT QLHPEFRDLT PDYALTQKIF FPRNTIPRTE NRQLAIDVSL
EGSVEAVPIV EKRMFPLPEV PIGEANSISR VMNIFKEKRE ESMQKKLEHD RQAEANRLKS
AGLSASKAEQ EVCNSAQDRK EEKERTTEPA GKQQRTEDLV VIEGNQDEGD SDPQKKVDEK
TVPGESKQHS KSSGSSSTNQ MSQKVVDVPS VEDSSDQAPG DFPDYGYYFK RIVMDESGTV
LTEEAQLEKR QLLFIEVGYQ TDVDGKITTD YKKWKDILRL LELLNIKCSF IACADCSSTP
SNNWWISEDK VRLLKNSISH LFSKLTQNSP ADVTDIVVGS ISTQKVRSYL KSGTATKTPI
SLKDVQETWS KMKDYIVNRP TGISLNKELV GALYQGLVEG AIISKEGTVN LIQMLKDKQE
RITDEFERTK LKHEVNEDVK TSEKLLLGWL MEDLKGCRCM GCLTKIKELS ESMSVNQDRL
EYLSTNCQTK SHCTECHPRS LEYRNISNVD NRVPSMQRVS HSRNEGFEDT NETLTELDRL
VRLTLPGKTE KERRVKRNVE GLIRFMMQQS SLDCIKLPSG QIIAHRCSKK FKNSSEAEEK
CNERFERLMK ELSEQKLKPY SDHVRKTITS SLKKTDKQAG SKCAVPRLWL ETLIRDLRVP
TKDEEILLNI RTSMQSKTNF IRNNDKLIIR SNKEIADYLE TKRKNLLSEK ASDKIFSSDC
ILFKEVIAEA LRRYYSTPYE GVPETIVKLI NFLCTFGWFQ EVVLYSKICE TFLRCCTEFS
RSGIKLVKVR HCDTNLSIKL PSNKKENMLC CLYDKNMSLL KGPFFLNRRQ AILGSAYPYI
LITLYIQVLQ QHRCLEVLNS VNDRVVGNIN TCTSNLLNTV KAELTLVNSG LFEKAYECRT
EQCRLGGNFL NRSSRDHFIS TVSGLNVVYG ALIKDNLLAN SQPQNKQLQM LRFGMLCGLS
RLSSALELGK KFSTSCRRIE DNIMRLYLQS TIYSANRDVS QNVQNWKMKD LCPDITIPCF
SVYGLFVNSD RQRIFDIYNV HIYNKEMDNF DEGCITVLEE TAERHMLWEL DLLRSLEGDT
RDVRAARLLL GCPNIRKATD KDGNRLMKKG ITDDWREEAG SDSSSISGRR SYASSGTRVK
SMFGKYNSSQ KPFELKPGLE VVNDPLHDYK QAVQDSFCYS EYTPNTESVL KDCIHIIRTN
PSHTMGSYEL IQAVTENARR KYPPENIERA RKDPKNWVSI SEVTETTSIV SQPRTHFMLK
DCYKVLLGTE NKKIVKMLRG KLKKLGAMRT DIEIGKKDCL DLLTTVDGLS EEQCKNIVNG
IFEPSKLSFY HWKDLLKKEL SEVLLTDDGN YIYCWLKTLS SMVKHSLKKD LRFMTGKNSL
DIKPEMFTDE EYSALNIMKL ELLGEHTDGI QGKTDFLLSS WKKCALKPKE GQSILNVGLN
SLAALHDELY DIRLQHLELT RIKKENPTVS FTKEEILVKR LEKGFLNKYK KEVMEAVNLI
FYCCLTAPWC LHYKSLEAYL VRHPEILETE CIKENDIPLL DLTVTSLIRS LIDDIEGESS
FNDSSDIKVR FAVKYLITLF TANGEPFSLS LNDGGLNDDL QLTTDEKLLY QTKKVFAKLG
LSGNNYDFIW TLQMIANSNF NVCKRLTGRT TGERLPRSVR SKVIYEMVKL VGETGMAILQ
QLAFSQALNY DHRFYAVLAP KAQLGGSRDL LVQETGTKVI HATTEMFSRN LLKTTSDDGL
TNPHLKETRL NIGLDMLSTA RALDGKQVSD DSNLLNFFKT VCISGDNTKW GPIHCCSFFS
GMMQQLLKDV QDWSSFYKLT FIKNLCRQIE IPAPSIRKIL NVLRFKLSDK GGVEKLSEEA
IRSELINNLA EWEGNDTVKF LITTYISKGI MAMNSYNHMG QGIHHATSSL LTSMMAETFE
ELAVDYMKKH FPGLTVNVDH AGSSDDYAKC IIVSGLVSKD MYKRYDGVFW RHMCRLKNFL
AAVRRCCQMK DSAKTLVGDC FLEFYSEFMM GNRVTPAVIK FIFTGLINSS VTSPQSLVQA
CHVSSQQGMY NSVPLVTNAA FTILRQQIFY NHVEDFIRRY GLITLGAVSP FGRLFLPRFS
GLVSSSVALE DSETISKAAA EINSNDIFFN TSSLSNLDKL EQSPDSSGLD DDSVVSTTTV
ESSDSKGSSS SFTFDLNRPL SETEVKFLKL LRELTSTTAC EMLQEKINTL YNDSREGPLD
RHNILQNCRL SESCDWLLDG KKRGLLELSR RMSCLLNVLI AGYYRSFGSE GTEKQVKASW
SRDDNRVIED PMIQLIPEKL RRELERLGLS RMEVDELMPA VGPDESLSQL VAKKLISLNV
STEEYSAEVS RLKQTLTARN VLHGLAGGIK ELSLPIYTIF MKPYFFKDNV FLDLEDRWSS
RHSTNYRDST GKMLTGKVVT KFTHWLDTFL SCVVSANRSQ EIKECSLFNP NLRCVNIMVK
GNGIKELSYI RSHLSVLSVE FENLNLQFSD VNRQKLKIVE SRPPECELEA NKAVIIKSKL
FSAVEHVRLS NNPAVVMGYL LEESSISEVK PTKVDFSNLL KHRFKLMQFF PSVFTLLRSL
QSESKELEKL GEPVDMHQVS KYANHLTLLC RMIQQSKPSL TVFYMLKGSQ MNTEPTVSEL
VSYGIKEGRF LKLPEIGLDA STYSVRYWKI LHCISAIGEL PLSSEDKTSL LISFLNWKVT
SDCVDDCCPL EKYDKAIVSE FSGQVLINTL ASELSSVRKD QEREGLTDLI DYINSPSELL
KKKPYLGTTC RFQCWGEGAK SGKFTYSSRT GEAIGIFVAG KLHIHLTSDS PGLLCEVERQ
VLSWLGKRRT DVLTKEQHQF FLDFLPNLSE VVQKNRDGAI LGVTIDSTNV RMLKYVPPKR
NTPVIKIKKQ ILTVKKQTTL DVESEPRIVW GHGQLSIVYD ECETETTYHE NLIKVKKLVD
LASGTTDKLP TAIFSDTRIT LARVKFKTEL LLNSLCLLHC FLKHTSQDAI QEVESKCNVL
ERYLRSGGVQ FRPMSESLDK KVTKLPLQCQ SDKDVDKEIN FCEDLTRVFS NENVPLSSWS
EVQSYIEEVG FGNVLVHIEK NPTRSDLIWR FSIDSISGNF GPIKDIRTLV TYMSTETVPK
FLLPFLLFEE QLKHLIAGCV ELRDALNSSG INDREIAIVA LFTCFYYQSD SVKRQGPVCS
ISSFCSLIGD DLLPLDNRLQ ARVLPEQDNV KLHFKLNLTT DSALGKKDKA IQAKKIISRY
LRLIFTEDDM DLKRLKSDAT KVKLSSEKEC EFLEFCLHSD LSYALNYRVL LEHLIDLEDR
AKKTACVLIE EFILMLTGRL MISSTIDSDS KRTLEDDALC LEDLLDSDNE ASSSKSDNEE
QIALQTGKFN FNWDSD
