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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: 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).By similarity
NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity (By similarity).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).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.PROSITE-ProRule annotation
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).PROSITE-ProRule annotation

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.PROSITE-ProRule annotation
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei1038For 3CLpro activityPROSITE-ProRule annotation1
Active sitei1062For 3CLpro activityPROSITE-ProRule annotation1
Active sitei1147For 3CLpro activityPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi495 – 502ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

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 virusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000007767 Componenti: Genome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003419981 – 1699Genome polyproteinAdd BLAST1699
ChainiPRO_00000369141 – 330Protein p37Add BLAST330
ChainiPRO_0000036915331 – 696NTPaseAdd BLAST366
ChainiPRO_0000036916697 – 875Protein p20Add BLAST179
ChainiPRO_0000036917876 – 1007Viral genome-linked proteinAdd BLAST132
ChainiPRO_00000369181008 – 11893C-like proteaseAdd BLAST182
ChainiPRO_00000369191190 – 1699RNA-directed RNA polymeraseAdd BLAST510

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei902O-(5'-phospho-RNA)-tyrosineBy similarity1

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. 3CLpro is first autocatalytically cleaved, then processes the whole polyprotein.PROSITE-ProRule annotation
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).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei330 – 331Cleavage; by 3CLproBy similarity2
Sitei696 – 697Cleavage; by 3CLproBy similarity2
Sitei875 – 876Cleavage; by 3CLproBy similarity2
Sitei1008 – 1009Cleavage; by 3CLproBy similarity2
Sitei1189 – 1190Cleavage; by 3CLproBy similarity2

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Proteomic databases

PRIDEiP54634.

Interactioni

Subunit structurei

Protein p37 interacts with human VAPA.By similarity

Structurei

3D structure databases

ProteinModelPortaliP54634.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini465 – 632SF3 helicasePROSITE-ProRule annotationAdd BLAST168
Domaini1009 – 1189Peptidase C37PROSITE-ProRule annotationAdd BLAST181
Domaini1425 – 1546RdRp catalyticPROSITE-ProRule annotationAdd BLAST122

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi69 – 73Poly-Pro5
Compositional biasi944 – 947Poly-Glu4

Sequence similaritiesi

Contains 1 peptidase C37 domain.PROSITE-ProRule annotation
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation
Contains 1 SF3 helicase domain.PROSITE-ProRule annotation

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.
IPR009003. Peptidase_S1_PA.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
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

« Hide

        10         20         30         40         50
MKMASNDASA AAVVNSNNDT AKSSSDGVLS SMAVTFKRAL GGRAKQPPPR
60 70 80 90 100
ETPQRPPRPP TPELVKKIPP PPPNGEDELV VSYSVKDGVS GLPELSTVRQ
110 120 130 140 150
PDEANTAFSV PPLNQRENRD AKEPLTGTIL EMWDGEIYHY GLYVERGLVL
160 170 180 190 200
GVHKPPAAIS LAKVELTPLS LFWRPVYTPQ YLISPDTLKR LHGESFPYTA
210 220 230 240 250
FDNNCYAFCC WVLDLNDSWL SRRMIQRTTG FFRPYQDWNR KPLPTMDDSK
260 270 280 290 300
LKKVANVFLC ALSSLFTRPI KDIIGKLRPL NILNILASCD WTFAGIVESL
310 320 330 340 350
ILLAELFGVF WTPPDVSAMI APLLGDYELQ GPEDLAVELV PIVMGGIGLV
360 370 380 390 400
LGFTKEKIGK MLSSAASTLR ACKDLGAYGL EILKLVMKWF FPKKEEANEL
410 420 430 440 450
AMVRSIEDAV LDLEAIENNH MTTLLKDKDS LATYMRTLDL EEEKARKLST
460 470 480 490 500
KSASPDIVGT INALLARIAA ARSLVHRAKE ELSSRLRPVV VMISGKPGIG
510 520 530 540 550
KTHLARELAK RIAASLTGDQ RVGLIPRNGV DHWDAYKGER VVLWDDYGMS
560 570 580 590 600
NPIHDALRLQ ELADTCPLTL NCDRIENKGK VFDSDAIIIT TNLANPAPLD
610 620 630 640 650
YVNFEACSRR IDFLVYAEAP EVEKAKRDFP GQPDMWKNAF SPDFSHIKLA
660 670 680 690 700
LAPQGGFDKN GNTPHGKGVM KTLTTGSLIA RASGLLHERL DEYELQGPAL
710 720 730 740 750
TTFNFDRNKV LAFRQLAAEN KYGLMDTMKV GRQLKDVRTM PELKQALKNI
760 770 780 790 800
SIKRCQIVYS GCTYTLESDG KGNVKVDRVQ SATVQTNHEL AGALHHLRCA
810 820 830 840 850
RIRYYVKCVQ EALYSIIQIA GAAFVTTRIV KRMNIQDLWS KPQVEDTEDT
860 870 880 890 900
ANKDGCPKPK DDEEFVVSSD DIKTEGKKGK NKTGRGKKHT AFSSKGLSDE
910 920 930 940 950
EYDEYKRIRE ERNGKYSIEE YLQDRDKYYE EVAIARATEE DFCEEEEAKI
960 970 980 990 1000
RQRIFRPTRK QRKEERASLG LVTGSEIRKR NPDDFKPKGK LWADDDRSVD
1010 1020 1030 1040 1050
YNEKLDFEAP PSIWSRIVNF GSGWGFWVSP SLFITSTHVI PQGAQEFFGV
1060 1070 1080 1090 1100
PVKQIQIHKS GEFCRLRFPK PIRTDVTGMI LEEGAPEGTV VTLLIKRSTG
1110 1120 1130 1140 1150
ELMPLAARMG THATMKIQGR TVGGQMGMLL TGSNAKSMDL GTTPGDCGCP
1160 1170 1180 1190 1200
YIYKRENDYV VIGVHTAAAR GGNTVICATQ GSEGEATLEG GDNKGTYCGA
1210 1220 1230 1240 1250
PILGPGSAPK LSTKTKFWRS STAPLPPGTY EPAYLGGKDP RVKGGPSLQQ
1260 1270 1280 1290 1300
VMRDQLKPFT EPRGKPPKPS VLEAAKRTII NVLEQTIDPP QKWSFTQACA
1310 1320 1330 1340 1350
SLDKTTSSGH PHHMRKNDCW NGESFTGKLA DQASKANLMF EEGKNMTPVY
1360 1370 1380 1390 1400
TGALKDELVK TDKIYGKIKK RLLWGSDLAT MIRCARAFGG LMDELKAHCV
1410 1420 1430 1440 1450
TLPIRVGMNM NEDGPIIFER HSRYKYHYDA DYSRWDSTQQ RAVLAAALEI
1460 1470 1480 1490 1500
MVKFSPEPHL AQIVAEDLLS PSVMDVGDFK ISINEGLPSG VPCTSQWNSI
1510 1520 1530 1540 1550
AHWLLTLCAL SEVTNLSPDI IQANSLFSFY GDDEIVSTDI NLNPEKLTAK
1560 1570 1580 1590 1600
LKEYGLKPTR PDKTEGPLII SEDLNGLTFL RRTVTRDPAG WFGKLDQSSI
1610 1620 1630 1640 1650
LRQMYWTRGP NHEDPSETMI PHSQRPIQLM SLLGEAALHG PAFYSKISKL
1660 1670 1680 1690
VIAELKEGGM DFYVPRQEPM FRWMRFSDLS TWEGDRNLAP SFVNEDGVE
Length:1,699
Mass (Da):189,201
Last modified:October 1, 1996 - v1
Checksum:iFA00B3B67FF3A0B6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X86557 Genomic RNA. Translation: CAA60254.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X86557 Genomic RNA. Translation: CAA60254.1.

3D structure databases

ProteinModelPortaliP54634.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC37.001.

Proteomic databases

PRIDEiP54634.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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.
IPR009003. Peptidase_S1_PA.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
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]
ProtoNetiSearch...

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: October 5, 2016
This is version 96 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.