Q2Y2L8 · L_AMPV1

Function

function

Responsible for RNA synthesis (replicase and transcriptase), cap addition, and cap methylation. Performs also the polyadenylation of subgenomic mRNAs by a stuttering mechanism at a slipery stop site present at the end of viral genes. The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The viral polymerase binds to the genomic RNA at two different sites in the 3' leader promoter thereby initiating either genome replication or mRNA transcription. In the transcription mode, the polymerase performs the sequential transcription of all mRNAs using a termination-reinitiation mechanism responding to gene start and gene end signals. Some polymerase disengage from the template at each gene junction, resulting in a decreasing abundance of transcripts from the 3' to the 5' end of the genome. The first gene is the most transcribed, and the last the least transcribed. Needs as cofactors the phosphoprotein for processivity and the M2-1 anti-termination protein. Polyribonucleotidyl transferase (PRNTase) adds the cap structure when the nascent RNA chain length has reached few nucleotides (By similarity).
Ribose 2'-O methylation of viral mRNA cap precedes and facilitates subsequent guanine-N-7 methylation (By similarity).
In the replication mode, the polymerase replicates the whole viral genome without recognizing the gene end transcriptional signals. The ability of the polymerase to override the gene end signals as it is producing the antigenome is probably due to replicative RNA becoming encapsidated with nucleoprotein as it is synthesized (By similarity).

Catalytic activity

  • a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1)
    EC:2.7.7.48 (UniProtKB | ENZYME | Rhea)
  • GTP + H2O = GDP + H+ + phosphate
  • a 5'-end triphospho-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + GDP + H+ = a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + diphosphate
    EC:2.7.7.88 (UniProtKB | ENZYME | Rhea)
  • a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + 2 S-adenosyl-L-methionine = a 5'-end (N7-methyl 5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + H+ + 2 S-adenosyl-L-homocysteine
    EC:2.1.1.375 (UniProtKB | ENZYME | Rhea)
  • a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-methionine = a 5'-end (5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + H+ + S-adenosyl-L-homocysteine
  • a 5'-end (5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-methionine = a 5'-end (N7-methyl 5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-homocysteine

Cofactor

Mg2+ (UniProtKB | Rhea| CHEBI:18420 )

Note: For RNA-directed RNA polymerase activity. Mn2+ can stimulate de novo initiation but it is inefficient at supporting elongation of de novo initiated RNA.

Features

Showing features for binding site, active site.

TypeIDPosition(s)Description
Binding site635Mg2+ (UniProtKB | ChEBI); catalytic; for RNA-directed RNA polymerase activity
Binding site745Mg2+ (UniProtKB | ChEBI); catalytic; for RNA-directed RNA polymerase activity
Active site1263Nucleophile; for GDP polyribonucleotidyltransferase activity
Active site1673For mRNA (nucleoside-2'-O-)-methyltransferase activity
Binding site1696-1700substrate; for mRNA (nucleoside-2'-O-)-methyltransferase activity
Active site1779For mRNA (nucleoside-2'-O-)-methyltransferase activity
Active site1817For mRNA (nucleoside-2'-O-)-methyltransferase activity
Active site1848For mRNA (nucleoside-2'-O-)-methyltransferase activity

GO annotations

AspectTerm
Cellular Componenthost cell cytoplasm
Cellular Componentvirion component
Molecular FunctionATP binding
Molecular FunctionGTPase activity
Molecular Functionmetal ion binding
Molecular FunctionmRNA 5'-cap (guanine-N7-)-methyltransferase activity
Molecular FunctionRNA-dependent RNA polymerase activity

Keywords

Names & Taxonomy

Protein names

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

Including 4 domains:

  • Recommended name
    RNA-directed RNA polymerase
  • EC number
  • Recommended name
    GTP phosphohydrolase
  • EC number
  • Recommended name
    GDP polyribonucleotidyltransferase
  • EC number
  • Alternative names
    • PRNTase
  • Recommended name
    mRNA cap methyltransferase
  • EC number
  • Alternative names
    • mRNA (guanine-N(7)-)-methyltransferase
      (G-N7-MTase
      )
    • mRNA (nucleoside-2'-O-)-methyltransferase
      (N1-2'-O-MTase
      )

Gene names

    • Name
      L

Organism names

Accessions

  • Primary accession
    Q2Y2L8

Proteomes

Subcellular Location

Virion
Host cytoplasm
Note: Localizes in cytoplasmic inclusion bodies.

Keywords

PTM/Processing

Features

Showing features for chain.

TypeIDPosition(s)Description
ChainPRO_00003903641-2005RNA-directed RNA polymerase L

Interaction

Subunit

Interacts with the phosphoprotein (via C-terminus); the association of P and L forms the polymerase complex.

Structure

3D structure databases

Family & Domains

Features

Showing features for domain, region.

TypeIDPosition(s)Description
Domain628-811RdRp catalytic
Region902-1379GDP polyribonucleotidyltransferase
Domain1662-1857Mononegavirus-type SAM-dependent 2'-O-MTase

Domain

Contains an RNA-dependent RNA polymerase (RdRp) domain, a polyribonucleotidyl transferase (PRNTase or capping) domain and a methyltransferase (MTase) domain.

Sequence similarities

Belongs to the paramyxovirus L protein family.

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    2,005
  • Mass (Da)
    228,894
  • Last updated
    2021-02-10 v2
  • Checksum
    D6C87E72A95BF80B
MDPLNEGVVNVYLTDSYLKGVISFSETNAIGSCLLGKHYLKKDNTSKVAIESPVVEHIRLRNAFQTRIKEKNLRVVEPVNMQSEVMRNSYTCELNLLKQLITRSKDISSLKLDMICDWLQLKSTSENPSVLKFVDVRCIPDWVSTWFSSWYNLNKLILEFRREEVACTGSIICKTIGSIMFIISSFGCVIKSNKSKRISFMTYNQVLTWKDVMLSRFNANLCVWISNSLNKNQEGLGLRSNLQGALVNKLYEIVDSMLSVCSNEGFTLVKEFEGFIMSEILKITEHAQFSTRFRNTLLNGLVDQLAKMRGLNRKRVSGTVLEGNQYPMYETTLATLGGALKTIRLLVNKNLDNAAELYYIFRIFGHPMVEEREAMDAVRLNNEITKILKLESLTELRGAFILRIIKGFVDTNKRWPKIKNLKVLSRRWIMYFKAKSYPSQLELSSQDFLELAGVQFEQEFAIPERTNLEMVLNDKAISPPKNLIWSVFPKNYLPTNIRERFTEEMFNSSEKLKTRRVLEYYLKDNKFDQNDLKKYVVRQEYLGDKEHVVSLTGKERELSVGRMFAMQPGKQRQVQILAEKLLADNIVPFFPETLTKYGDLELQRIMEIKSELSSVKSRRNDSYNNYIARASIVTDLSKFNQAFRYETSSVCADVVDELHGTQSLFCWLHLTVPLTTMICTYRHAPPETEGVYDIDKIKEQSGLYRFHMGGIEGWCQKLWTMEAVSLLDVVSVKNRVQLTSLLNGDNQSIDVSKPVRLSQGVDEVKADYSLAVKMLKEIRNAYKDIGHKLKEGETYISRDLQFMSKVIQSEGVMHPSPIKKILRVGPWINTILDDIKTSAESIGSLCQELEFRGESLLVSLILRNFWLYELWMHESKSHPLAGKQLYRQLSKTLAITQKFFGITKETDVVNLWMNVPMQFGGGDPVVLYRSFYRRTPDFLTEAVSHMSVLLKVYGKAKEGSKKDFFKALLSVDKNKRATLTTLMRDPQAVGSERQARVTSEINRAAVTSVLSLSPNQLFCDSAIHYSRNEEEVGLIAQNITPVYPHGLRVLYESLPFHKAEKVVNMISGTKSITNLLQRTSAINGEDIDRAVSMMLENLGLLSRILSVCQDDITLPTKANGDLICCQVSRTLRERSWDNMEIVGVTSPSIVTCMNIVYSSSSQLKGITIEKFSTDKTTRGQRGPKSPWVGSSTQEKKLVPVYNRQILSKQQKEQLEAIGKLRWVYKGTQGLRRLLDKICIGSLGISYKNVKPLLPRFMSVNFLHRLSVSSRPMEFPASVPAYRTTNYHFDTSPVNQTLSERFGNEDINLVFQNAISCGISVMSVVEQLTGRSPKQLVMIPQLEEIDIMPPPVFLGKFDYKLVEKISSDQHIFSPDKLDLVTLGKMLMPSTSGAKSDQFWNRKENFFHGNNLVESLSAALACHWCGILTEQCNENNIFRREWGDGFVTDHAFIDFKTFVGVFKTKLLCGWGSRGGDIKDRDMIDESIDKLIRVDNSFWRMFSKVILEPKVRKRVMLFDVKILSLVGYAGFKNWFIDHLRSSDLCEVPWVVNADSEIVEVSAVKIYLQLLRVSSPLRITVLNYSDMAHAITRLIRRKSMHDNVPSISRTLSPAELAPVVEPTVQMNLFPKITFERLKNYETVSGSTRGKLTRNYMVMLPWQHINRFNFVFSSTGCKISVKACIGRLIQDLNPTVFYFVGEGAGNWMARTACEYPNAKFVYRSLKDDLDHHFPLEFQRVLGNMNRVIDGGEGLSMDTTDATQKTHWDLIHRICKDALLITLCDAEFKDRDDFFKMVTLWRKHVLSCRICTTYGTDLYLFAKYHAKEQSIKLPYFVRSIATYVMQGSKLSGSECYVLLTLGHHNNLPCHGEVQSSKLKLAVCNDFSIPRKVEVKAVEANCKSLLSGLRTPINRAELDRQKKMLTLRSYHSSVATVGGSRVIESKWLSKKATTIIEWLEHILNSPKGELNYDFFEALENTYPNMVKLLDNLGSAELKKLIKVTGYMLMSKK

Sequence caution

The sequence AAY82583.1 differs from that shown. Reason: Frameshift

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
DQ009484
EMBL· GenBank· DDBJ
AAY82583.1
EMBL· GenBank· DDBJ
Viral cRNA Frameshift

Similar Proteins

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