J3TRD1 · L_HTRV

  • Protein
    RNA-directed RNA polymerase L
  • Gene
    L
  • Status
    UniProtKB reviewed (Swiss-Prot)
  • Amino acids
  • Protein existence
    Evidence at protein level
  • Annotation score
    5/5

Function

function

RNA-dependent RNA polymerase, which is responsible for the replication and transcription of the viral RNA genome using antigenomic RNA as an intermediate (By similarity).
During transcription, synthesizes subgenomic RNAs and assures their capping by a cap-snatching mechanism, which involves the endonuclease activity cleaving the host capped pre-mRNAs (PubMed:31914382).
These short capped RNAs are then used as primers for viral transcription. The 3'-end of subgenomic mRNAs molecules are not polyadenylated. During replication, the polymerase binds the 5' and 3' vRNA extremities at distinct sites (By similarity).
In turn, significant conformational changes occur in the polymerase and in vRNA to initiate active RNA synthesis (By similarity).
As a consequence of the use of the same enzyme for both transcription and replication, these mechanisms need to be well coordinated (By similarity).

Miscellaneous

Classified as His+ endonuclease since it has a histidine upstream of the active site that coordinates the first cation.

Catalytic activity

Cofactor

Protein has several cofactor binding sites:
Mn2+ (UniProtKB | Rhea| CHEBI:29035 )

Note: For endonuclease activity. Binds 2 Mn2+ ions in the active site (By similarity).
The divalent metal ions are crucial for catalytic activity (PubMed:31948728).
Mg2+ (UniProtKB | Rhea| CHEBI:18420 )

Mn2+ (UniProtKB | Rhea| CHEBI:29035 )

Note: For polymerase activity. Initiation activity is stronger in the presence of Mn2+ than in the presence of Mg2+.

Activity regulation

Inhibited by Baloxavir acid (BXA).

Features

Showing features for binding site, active site, site.

TypeIDPosition(s)Description
Binding site80Mn2+ 1 (UniProtKB | ChEBI)
Binding site112Mn2+ 1 (UniProtKB | ChEBI)
Binding site112Mn2+ 2 (UniProtKB | ChEBI)
Binding site126Mn2+ 1 (UniProtKB | ChEBI)
Active site145For endonuclease activity
Binding site1127Mg2+ (UniProtKB | ChEBI); catalytic; for RdRp activity
Site1703Interaction with the cap substrate
Site1707Interaction with the cap substrate
Site1719Interaction with the cap substrate
Site1772Interaction with the cap substrate

GO annotations

AspectTerm
Cellular Componenthost cell endoplasmic reticulum
Cellular Componenthost cell endoplasmic reticulum-Golgi intermediate compartment
Cellular Componenthost cell Golgi apparatus
Cellular Componentvirion component
Molecular Functionhydrolase activity
Molecular Functionmetal ion binding
Molecular Functionnucleotide binding
Molecular FunctionRNA-dependent RNA polymerase activity
Biological ProcessDNA-templated transcription
Biological Processviral RNA genome replication

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    RNA-directed RNA polymerase L
  • EC number
  • Short names
    Protein L
  • Alternative names
    • Large structural protein
    • Replicase
    • Transcriptase

Including 1 domain:

  • Recommended name
    cap-snatching endonuclease
  • EC number

Gene names

    • Name
      L

Organism names

Accessions

  • Primary accession
    J3TRD1

Proteomes

PTM/Processing

Features

Showing features for chain.

TypeIDPosition(s)Description
ChainPRO_00004560601-2084RNA-directed RNA polymerase L

Interaction

Subunit

Homomultimer (By similarity).
Interacts with glycoprotein N; this interaction allows efficient polymerase packaging into virus particles (By similarity).
Interacts with nucleoprotein N (By similarity).

Structure

3D structure databases

Family & Domains

Features

Showing features for region, domain.

TypeIDPosition(s)Description
Region20-221Endonuclease
Domain969-1172RdRp catalytic
Region1696-1810Cap-binding

Domain

The N-terminus contains the endonuclease activity (endoN) (By similarity).
The central region contains the RdRp activity (By similarity).
The C-terminus contains the cap-binding region (By similarity).

Sequence similarities

Belongs to the Bunyavirales RNA polymerase family.

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    2,084
  • Mass (Da)
    236,364
  • Last updated
    2012-10-31 v1
  • Checksum
    E4070623FEBE9533
MNLEALCSRVLSERGLSTGEPGVYDQIFERPGLPNLEVTVDSTGVVVDVGAIPDSASQLGSSINAGVLTIPLSEAYKINHDFTFSGLTKTTDRKLSEVFPLVHDGSDSMTPDVIHTRLDGTVVVIEFTTTRSTNMGGLEAAYRSKLEKYRDPLNRRTDIMPDASIYFGIIVVSASGVLTNMPLTQDEAEELMFRFCVANEIYSQARAMDAEVELQKSEEEYEAISRARAFFTLFDYDDGKLSEAFPNSDIEMLRRFLSQPVDTSFVTTTLKEKEQEAYKRMCEEHYLKSGMSTKERLEANRSDAIDKTRALMERLHNMSSKELHSNKSTVKLPPWVVKPSDRTLDVKTDTGSGELLNHGPYGELWSRCFLEIVLGNVEGVISSPEKELEIAISDDPEADTPKAAKIKYHRFRPELSLESKHEFSLQGIEGKRWKHSARNVLKDEMSHKTMSPFVDVSNIEEFLIMNNLLNDTSFNREGLQETINLLLEKATEMHQNGLSTALNDSFKRNFNTNVVQWSMWVSCLAQELASALKQHCKPGEFIIKKLMHWPIFVIIKPTKSSSHIFYSLAIKKANIKRRLIGDVFTDTIDAGEWEFSEFKSLKTCKLTNLINLPCTMLNSIAFWREKMGVAPWISRKACSELREQVAITFLMSLEDKSTTEELVTLTRYSQMEGFVSPPLLPKPQKMVEKLEVPLRTKLQVFLFRRHLDAIVRVAASPFPIVARDGRVEWTGTFNAITGRSTGLENMVNNWYIGYYKNKEESTELNALGEMYKKIVEIEAEKPTSSEYLGWGDTSSPKRHEFSRSFLKSACISLEKEIEMRHGKSWKQSLEERVLKELGSKNLLDLATMKATSNFSKEWEAFSEVRTKEYHRSKLLEKMAELIEHGLMWYVDAAGHAWKAVLDDKCMRICLFKKNQHGGLREIYVTNANARLVQFGVETMARCVCELSPHETIANPRLKSSIIENHGLKSARQLGQGTINVNSSNDAKKWSQGHYTTKLAMVLCWFMPAKFHRFIWAGISMFRCKKMMMDLRFLEKLSTKANQKTDDDFRKDLAGAFHGNVEVPWMTQGATYLQTETGMMQGILHFTSSLLHSCVQSFYKAYFLSRLKEGIAGRTIKAAIDVLEGSDDSAIMISLKPASDNEEAMARFLTANLLYSVRVINPLFGIYSSEKSTVNTLFCVEYNSEFHFHKHLVRPTIRWVAASHQISESEALASRQEDYANLLTQCLEGGSSFSLTYLIQCAQLVHHYMLLGLCLHPLFGTFVGMLIEDPDPALGFFIMDNPAFAGGAGFRFNLWRSCKFTNLGKKYAFFFNEIQGKTKGDADYRALDATTGGTLSHSVMTYWGDRRKYQHLLDRMGLPKDWVERIDENPSILYRRPENKQELILRLAEKVHSPGVTSSFSKGHVVPRVVAAGVYLLSRHCFRYTASIHGRGASQKASLIKLLVMSSTSAERNQGRLNPNQERMLFPQVQEYERVLTLLDEVTALTGKFVVRERNIVKSRVELFQEPVDLRCKAENLIAEMWFGLKRTKLGPRLLKEEWDKLRASFSWLSTDHKETLDVGPFLSHVQFRNFIAHVDAKSRSVRLLGAPVKKSGGVTTVSQVVKSNFFPGFILDSSESLDDQERVEGVSILKHILFMTLNGPYTDEQKKAMVLETFQYFALPHAAEVVKRSRSLTLCLMKNFIEQRGGSILDQIEKAQSGTVGGFSKPQKPYRKQSGGIGYKGKGVWSGIMENTNVQILIDGDGSSNWIEEIRLSSESRLFDVIESVRRLCDDINVNNRVTSSFRGHCMVRLSNFKVKPASRVEGCPVRLMPSSFRIKELQNPDEVFLRVRGDILNLSILLQEDRVMNLLSYRARDTDISESAASYLWMNRTDFSFGKKEPSCSWMCLKTLDSWAWNQAARVLERNIKTPGIDNTAMGNIFKDCLESSLRKQGLLRSRIAEMVERHVIPLTSQELVDILEEDVDFSEMMQSDIMEGDLDIDILMEGSPMLWAAEVEEMGEAMVILSQSGKYYHLKLMDQAATTLSTILGKDGCRLLLGRPTGRSNLREQVKPYLTLLQIREGDVNWVSEYKDDTRGLDEDSAEMWG

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
JX005846
EMBL· GenBank· DDBJ
AFP33395.1
EMBL· GenBank· DDBJ
Genomic RNA

Genome annotation databases

Similar Proteins

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