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P54634

- POLG_LORDV

UniProt

P54634 - POLG_LORDV

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Protein
Genome polyprotein
Gene
ORF1
Organism
Lordsdale virus (strain GII/Human/United Kingdom/Lordsdale/1993) (Human enteric calicivirus) (Hu/NV/LD/1993/UK)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

Protein p37 may play a role in viral replication by interacting with host VAPA, a vesicle-associated membrane protein that plays a role in SNARE-mediated vesicle fusion. This interaction may target replication complex to intracellular membranes By similarity.
NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity By similarity.
Protein P20 may play a role in targeting replication complex to intracellular membranes By similarity.
Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation By similarity.
3C-like protease processes the polyprotein: 3CLpro-RdRp is first released by autocleavage, then all other proteins are cleaved. May cleave polyadenylate-binding protein thereby inhibiting cellular translation By similarity.
RNA-directed RNA polymerase replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA codes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs By similarity.

Catalytic activityi

NTP + H2O = NDP + phosphate.
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|-Xaa and the P1' position is occupied by Gly-|-Yaa.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei330 – 3312Cleavage; by 3CLpro By similarity
Sitei696 – 6972Cleavage; by 3CLpro By similarity
Sitei875 – 8762Cleavage; by 3CLpro By similarity
Sitei1008 – 10092Cleavage; by 3CLpro By similarity
Active sitei1038 – 10381For 3CLpro activity By similarity
Active sitei1062 – 10621For 3CLpro activity By similarity
Active sitei1147 – 11471For 3CLpro activity By similarity
Sitei1189 – 11902Cleavage; by 3CLpro By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi495 – 5028ATP Reviewed prediction

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. RNA binding Source: InterPro
  3. RNA helicase activity Source: InterPro
  4. RNA-directed RNA polymerase activity Source: UniProtKB-KW
  5. cysteine-type endopeptidase activity Source: InterPro
Complete GO annotation...

GO - Biological processi

  1. RNA-protein covalent cross-linking Source: UniProtKB-KW
  2. transcription, DNA-templated Source: InterPro
  3. viral RNA genome replication Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase

Keywords - Biological processi

Host-virus interaction, Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Protein family/group databases

MEROPSiC37.001.

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 6 chains:
Alternative name(s):
p40
Alternative name(s):
VPG
3C-like protease (EC:3.4.22.66)
Short name:
3CLpro
Alternative name(s):
Calicivirin
Gene namesi
ORF Names:ORF1
OrganismiLordsdale virus (strain GII/Human/United Kingdom/Lordsdale/1993) (Human enteric calicivirus) (Hu/NV/LD/1993/UK)
Taxonomic identifieri82658 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
ProteomesiUP000007767: Genome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 16991699Genome polyprotein
PRO_0000341998Add
BLAST
Chaini1 – 330330Protein p37
PRO_0000036914Add
BLAST
Chaini331 – 696366NTPase
PRO_0000036915Add
BLAST
Chaini697 – 875179Protein p20
PRO_0000036916Add
BLAST
Chaini876 – 1007132Viral genome-linked protein
PRO_0000036917Add
BLAST
Chaini1008 – 11891823C-like protease
PRO_0000036918Add
BLAST
Chaini1190 – 1699510RNA-directed RNA polymerase
PRO_0000036919Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei902 – 9021O-(5'-phospho-RNA)-tyrosine By similarity

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. 3CLpro is first autocatalytically cleaved, then processes the whole polyprotein By similarity.
VPg is uridylylated by the polymerase and is covalently attached to the 5'-end of the polyadenylated genomic and subgenomic RNAs. This uridylylated form acts as a nucleotide-peptide primer for the polymerase By similarity.

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Interactioni

Subunit structurei

Protein p37 interacts with human VAPA By similarity.

Structurei

3D structure databases

ProteinModelPortaliP54634.
SMRiP54634. Positions 1009-1188, 1195-1695.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini465 – 632168SF3 helicase
Add
BLAST
Domaini1009 – 1189181Peptidase C37
Add
BLAST
Domaini1425 – 1546122RdRp catalytic
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi69 – 735Poly-Pro
Compositional biasi944 – 9474Poly-Glu

Sequence similaritiesi

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR001665. Norovirus_pept_C37.
IPR027417. P-loop_NTPase.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
IPR013614. Viral_PP_Calicivir_N.
[Graphical view]
PfamiPF08405. Calici_PP_N. 1 hit.
PF05416. Peptidase_C37. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00917. SRSVCYSPTASE.
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS51537. NV_3CL_PRO. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P54634-1 [UniParc]FASTAAdd to Basket

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MKMASNDASA AAVVNSNNDT AKSSSDGVLS SMAVTFKRAL GGRAKQPPPR     50
ETPQRPPRPP TPELVKKIPP PPPNGEDELV VSYSVKDGVS GLPELSTVRQ 100
PDEANTAFSV PPLNQRENRD AKEPLTGTIL EMWDGEIYHY GLYVERGLVL 150
GVHKPPAAIS LAKVELTPLS LFWRPVYTPQ YLISPDTLKR LHGESFPYTA 200
FDNNCYAFCC WVLDLNDSWL SRRMIQRTTG FFRPYQDWNR KPLPTMDDSK 250
LKKVANVFLC ALSSLFTRPI KDIIGKLRPL NILNILASCD WTFAGIVESL 300
ILLAELFGVF WTPPDVSAMI APLLGDYELQ GPEDLAVELV PIVMGGIGLV 350
LGFTKEKIGK MLSSAASTLR ACKDLGAYGL EILKLVMKWF FPKKEEANEL 400
AMVRSIEDAV LDLEAIENNH MTTLLKDKDS LATYMRTLDL EEEKARKLST 450
KSASPDIVGT INALLARIAA ARSLVHRAKE ELSSRLRPVV VMISGKPGIG 500
KTHLARELAK RIAASLTGDQ RVGLIPRNGV DHWDAYKGER VVLWDDYGMS 550
NPIHDALRLQ ELADTCPLTL NCDRIENKGK VFDSDAIIIT TNLANPAPLD 600
YVNFEACSRR IDFLVYAEAP EVEKAKRDFP GQPDMWKNAF SPDFSHIKLA 650
LAPQGGFDKN GNTPHGKGVM KTLTTGSLIA RASGLLHERL DEYELQGPAL 700
TTFNFDRNKV LAFRQLAAEN KYGLMDTMKV GRQLKDVRTM PELKQALKNI 750
SIKRCQIVYS GCTYTLESDG KGNVKVDRVQ SATVQTNHEL AGALHHLRCA 800
RIRYYVKCVQ EALYSIIQIA GAAFVTTRIV KRMNIQDLWS KPQVEDTEDT 850
ANKDGCPKPK DDEEFVVSSD DIKTEGKKGK NKTGRGKKHT AFSSKGLSDE 900
EYDEYKRIRE ERNGKYSIEE YLQDRDKYYE EVAIARATEE DFCEEEEAKI 950
RQRIFRPTRK QRKEERASLG LVTGSEIRKR NPDDFKPKGK LWADDDRSVD 1000
YNEKLDFEAP PSIWSRIVNF GSGWGFWVSP SLFITSTHVI PQGAQEFFGV 1050
PVKQIQIHKS GEFCRLRFPK PIRTDVTGMI LEEGAPEGTV VTLLIKRSTG 1100
ELMPLAARMG THATMKIQGR TVGGQMGMLL TGSNAKSMDL GTTPGDCGCP 1150
YIYKRENDYV VIGVHTAAAR GGNTVICATQ GSEGEATLEG GDNKGTYCGA 1200
PILGPGSAPK LSTKTKFWRS STAPLPPGTY EPAYLGGKDP RVKGGPSLQQ 1250
VMRDQLKPFT EPRGKPPKPS VLEAAKRTII NVLEQTIDPP QKWSFTQACA 1300
SLDKTTSSGH PHHMRKNDCW NGESFTGKLA DQASKANLMF EEGKNMTPVY 1350
TGALKDELVK TDKIYGKIKK RLLWGSDLAT MIRCARAFGG LMDELKAHCV 1400
TLPIRVGMNM NEDGPIIFER HSRYKYHYDA DYSRWDSTQQ RAVLAAALEI 1450
MVKFSPEPHL AQIVAEDLLS PSVMDVGDFK ISINEGLPSG VPCTSQWNSI 1500
AHWLLTLCAL SEVTNLSPDI IQANSLFSFY GDDEIVSTDI NLNPEKLTAK 1550
LKEYGLKPTR PDKTEGPLII SEDLNGLTFL RRTVTRDPAG WFGKLDQSSI 1600
LRQMYWTRGP NHEDPSETMI PHSQRPIQLM SLLGEAALHG PAFYSKISKL 1650
VIAELKEGGM DFYVPRQEPM FRWMRFSDLS TWEGDRNLAP SFVNEDGVE 1699
Length:1,699
Mass (Da):189,201
Last modified:October 1, 1996 - v1
Checksum:iFA00B3B67FF3A0B6
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X86557 Genomic RNA. Translation: CAA60254.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X86557 Genomic RNA. Translation: CAA60254.1 .

3D structure databases

ProteinModelPortali P54634.
SMRi P54634. Positions 1009-1188, 1195-1695.
ModBasei Search...

Protein family/group databases

MEROPSi C37.001.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Family and domain databases

Gene3Di 3.40.50.300. 1 hit.
InterProi IPR003593. AAA+_ATPase.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR001665. Norovirus_pept_C37.
IPR027417. P-loop_NTPase.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
IPR013614. Viral_PP_Calicivir_N.
[Graphical view ]
Pfami PF08405. Calici_PP_N. 1 hit.
PF05416. Peptidase_C37. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view ]
PRINTSi PR00917. SRSVCYSPTASE.
SMARTi SM00382. AAA. 1 hit.
[Graphical view ]
SUPFAMi SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEi PS51537. NV_3CL_PRO. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Human enteric Caliciviridae: the complete genome sequence and expression of virus-like particles from a genetic group II small round structured virus."
    Dingle K.E., Lambden P.R., Caul E.O., Clarke I.N.
    J. Gen. Virol. 76:2349-2355(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiPOLG_LORDV
AccessioniPrimary (citable) accession number: P54634
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: May 14, 2014
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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