Q2Y2L8 · L_AMPV1
- ProteinRNA-directed RNA polymerase L
- GeneL
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids2005 (go to sequence)
- Protein existenceInferred from homology
- Annotation score5/5
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).
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)
- GTP + H2O = GDP + H+ + phosphate
- 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
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.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 635 | Mg2+ (UniProtKB | ChEBI); catalytic; for RNA-directed RNA polymerase activity | ||||
Sequence: D | ||||||
Binding site | 745 | Mg2+ (UniProtKB | ChEBI); catalytic; for RNA-directed RNA polymerase activity | ||||
Sequence: D | ||||||
Active site | 1263 | Nucleophile; for GDP polyribonucleotidyltransferase activity | ||||
Sequence: H | ||||||
Active site | 1673 | For mRNA (nucleoside-2'-O-)-methyltransferase activity | ||||
Sequence: K | ||||||
Binding site | 1696-1700 | substrate; for mRNA (nucleoside-2'-O-)-methyltransferase activity | ||||
Sequence: GEGAG | ||||||
Active site | 1779 | For mRNA (nucleoside-2'-O-)-methyltransferase activity | ||||
Sequence: D | ||||||
Active site | 1817 | For mRNA (nucleoside-2'-O-)-methyltransferase activity | ||||
Sequence: K | ||||||
Active site | 1848 | For mRNA (nucleoside-2'-O-)-methyltransferase activity | ||||
Sequence: E |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | host cell cytoplasm | |
Cellular Component | virion component | |
Molecular Function | ATP binding | |
Molecular Function | GTPase activity | |
Molecular Function | metal ion binding | |
Molecular Function | mRNA 5'-cap (guanine-N7-)-methyltransferase activity | |
Molecular Function | RNA-dependent RNA polymerase activity |
Keywords
- Molecular function
- Biological process
- Ligand
Names & Taxonomy
Protein names
- Recommended nameRNA-directed RNA polymerase L
- Short namesProtein L
- Alternative names
Including 4 domains:
- Recommended nameRNA-directed RNA polymerase
- EC number
- Recommended nameGTP phosphohydrolase
- EC number
- Recommended nameGDP polyribonucleotidyltransferase
- EC number
- Alternative names
- Recommended namemRNA cap methyltransferase
- EC number
- Alternative names
Gene names
Organism names
- Taxonomic lineageViruses > Riboviria > Orthornavirae > Negarnaviricota > Haploviricotina > Monjiviricetes > Mononegavirales > Pneumoviridae > Metapneumovirus > Metapneumovirus avis
- Virus hosts
Accessions
- Primary accessionQ2Y2L8
Proteomes
Subcellular Location
UniProt Annotation
GO Annotation
Note: Localizes in cytoplasmic inclusion bodies.
Keywords
- Cellular component
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000390364 | 1-2005 | RNA-directed RNA polymerase L | |||
Sequence: MDPLNEGVVNVYLTDSYLKGVISFSETNAIGSCLLGKHYLKKDNTSKVAIESPVVEHIRLRNAFQTRIKEKNLRVVEPVNMQSEVMRNSYTCELNLLKQLITRSKDISSLKLDMICDWLQLKSTSENPSVLKFVDVRCIPDWVSTWFSSWYNLNKLILEFRREEVACTGSIICKTIGSIMFIISSFGCVIKSNKSKRISFMTYNQVLTWKDVMLSRFNANLCVWISNSLNKNQEGLGLRSNLQGALVNKLYEIVDSMLSVCSNEGFTLVKEFEGFIMSEILKITEHAQFSTRFRNTLLNGLVDQLAKMRGLNRKRVSGTVLEGNQYPMYETTLATLGGALKTIRLLVNKNLDNAAELYYIFRIFGHPMVEEREAMDAVRLNNEITKILKLESLTELRGAFILRIIKGFVDTNKRWPKIKNLKVLSRRWIMYFKAKSYPSQLELSSQDFLELAGVQFEQEFAIPERTNLEMVLNDKAISPPKNLIWSVFPKNYLPTNIRERFTEEMFNSSEKLKTRRVLEYYLKDNKFDQNDLKKYVVRQEYLGDKEHVVSLTGKERELSVGRMFAMQPGKQRQVQILAEKLLADNIVPFFPETLTKYGDLELQRIMEIKSELSSVKSRRNDSYNNYIARASIVTDLSKFNQAFRYETSSVCADVVDELHGTQSLFCWLHLTVPLTTMICTYRHAPPETEGVYDIDKIKEQSGLYRFHMGGIEGWCQKLWTMEAVSLLDVVSVKNRVQLTSLLNGDNQSIDVSKPVRLSQGVDEVKADYSLAVKMLKEIRNAYKDIGHKLKEGETYISRDLQFMSKVIQSEGVMHPSPIKKILRVGPWINTILDDIKTSAESIGSLCQELEFRGESLLVSLILRNFWLYELWMHESKSHPLAGKQLYRQLSKTLAITQKFFGITKETDVVNLWMNVPMQFGGGDPVVLYRSFYRRTPDFLTEAVSHMSVLLKVYGKAKEGSKKDFFKALLSVDKNKRATLTTLMRDPQAVGSERQARVTSEINRAAVTSVLSLSPNQLFCDSAIHYSRNEEEVGLIAQNITPVYPHGLRVLYESLPFHKAEKVVNMISGTKSITNLLQRTSAINGEDIDRAVSMMLENLGLLSRILSVCQDDITLPTKANGDLICCQVSRTLRERSWDNMEIVGVTSPSIVTCMNIVYSSSSQLKGITIEKFSTDKTTRGQRGPKSPWVGSSTQEKKLVPVYNRQILSKQQKEQLEAIGKLRWVYKGTQGLRRLLDKICIGSLGISYKNVKPLLPRFMSVNFLHRLSVSSRPMEFPASVPAYRTTNYHFDTSPVNQTLSERFGNEDINLVFQNAISCGISVMSVVEQLTGRSPKQLVMIPQLEEIDIMPPPVFLGKFDYKLVEKISSDQHIFSPDKLDLVTLGKMLMPSTSGAKSDQFWNRKENFFHGNNLVESLSAALACHWCGILTEQCNENNIFRREWGDGFVTDHAFIDFKTFVGVFKTKLLCGWGSRGGDIKDRDMIDESIDKLIRVDNSFWRMFSKVILEPKVRKRVMLFDVKILSLVGYAGFKNWFIDHLRSSDLCEVPWVVNADSEIVEVSAVKIYLQLLRVSSPLRITVLNYSDMAHAITRLIRRKSMHDNVPSISRTLSPAELAPVVEPTVQMNLFPKITFERLKNYETVSGSTRGKLTRNYMVMLPWQHINRFNFVFSSTGCKISVKACIGRLIQDLNPTVFYFVGEGAGNWMARTACEYPNAKFVYRSLKDDLDHHFPLEFQRVLGNMNRVIDGGEGLSMDTTDATQKTHWDLIHRICKDALLITLCDAEFKDRDDFFKMVTLWRKHVLSCRICTTYGTDLYLFAKYHAKEQSIKLPYFVRSIATYVMQGSKLSGSECYVLLTLGHHNNLPCHGEVQSSKLKLAVCNDFSIPRKVEVKAVEANCKSLLSGLRTPINRAELDRQKKMLTLRSYHSSVATVGGSRVIESKWLSKKATTIIEWLEHILNSPKGELNYDFFEALENTYPNMVKLLDNLGSAELKKLIKVTGYMLMSKK |
Interaction
Subunit
Interacts with the phosphoprotein (via C-terminus); the association of P and L forms the polymerase complex.
Family & Domains
Features
Showing features for domain, region.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 628-811 | RdRp catalytic | ||||
Sequence: ARASIVTDLSKFNQAFRYETSSVCADVVDELHGTQSLFCWLHLTVPLTTMICTYRHAPPETEGVYDIDKIKEQSGLYRFHMGGIEGWCQKLWTMEAVSLLDVVSVKNRVQLTSLLNGDNQSIDVSKPVRLSQGVDEVKADYSLAVKMLKEIRNAYKDIGHKLKEGETYISRDLQFMSKVIQSEG | ||||||
Region | 902-1379 | GDP polyribonucleotidyltransferase | ||||
Sequence: ITKETDVVNLWMNVPMQFGGGDPVVLYRSFYRRTPDFLTEAVSHMSVLLKVYGKAKEGSKKDFFKALLSVDKNKRATLTTLMRDPQAVGSERQARVTSEINRAAVTSVLSLSPNQLFCDSAIHYSRNEEEVGLIAQNITPVYPHGLRVLYESLPFHKAEKVVNMISGTKSITNLLQRTSAINGEDIDRAVSMMLENLGLLSRILSVCQDDITLPTKANGDLICCQVSRTLRERSWDNMEIVGVTSPSIVTCMNIVYSSSSQLKGITIEKFSTDKTTRGQRGPKSPWVGSSTQEKKLVPVYNRQILSKQQKEQLEAIGKLRWVYKGTQGLRRLLDKICIGSLGISYKNVKPLLPRFMSVNFLHRLSVSSRPMEFPASVPAYRTTNYHFDTSPVNQTLSERFGNEDINLVFQNAISCGISVMSVVEQLTGRSPKQLVMIPQLEEIDIMPPPVFLGKFDYKLVEKISSDQHIFSPDKLDLV | ||||||
Domain | 1662-1857 | Mononegavirus-type SAM-dependent 2'-O-MTase | ||||
Sequence: RFNFVFSSTGCKISVKACIGRLIQDLNPTVFYFVGEGAGNWMARTACEYPNAKFVYRSLKDDLDHHFPLEFQRVLGNMNRVIDGGEGLSMDTTDATQKTHWDLIHRICKDALLITLCDAEFKDRDDFFKMVTLWRKHVLSCRICTTYGTDLYLFAKYHAKEQSIKLPYFVRSIATYVMQGSKLSGSECYVLLTLGH |
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 statusComplete
- Length2,005
- Mass (Da)228,894
- Last updated2021-02-10 v2
- ChecksumD6C87E72A95BF80B
Sequence caution
Keywords
- Technical term