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P54634 (POLG_LORDV) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 89. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Genome polyprotein

Cleaved into the following 6 chains:

  1. Protein p37
  2. NTPase
    EC=3.6.1.15
    Alternative name(s):
    p40
  3. Protein p20
  4. Viral genome-linked protein
    Alternative name(s):
    VPG
  5. 3C-like protease
    Short name=3CLpro
    EC=3.4.22.66
    Alternative name(s):
    Calicivirin
  6. RNA-directed RNA polymerase
    Short name=RdRp
    EC=2.7.7.48
Gene names
ORF Names:ORF1
OrganismLordsdale virus (strain GII/Human/United Kingdom/Lordsdale/1993) (Human enteric calicivirus) (Hu/NV/LD/1993/UK) [Complete proteome]
Taxonomic identifier82658 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length1699 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred from homology

General annotation (Comments)

Function

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 activity

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).

Subunit structure

Protein p37 interacts with human VAPA By similarity.

Post-translational modification

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.

Sequence similarities

Contains 1 peptidase C37 domain.

Contains 1 RdRp catalytic domain.

Contains 1 SF3 helicase domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 16991699Genome polyprotein
PRO_0000341998
Chain1 – 330330Protein p37
PRO_0000036914
Chain331 – 696366NTPase
PRO_0000036915
Chain697 – 875179Protein p20
PRO_0000036916
Chain876 – 1007132Viral genome-linked protein
PRO_0000036917
Chain1008 – 11891823C-like protease
PRO_0000036918
Chain1190 – 1699510RNA-directed RNA polymerase
PRO_0000036919

Regions

Domain465 – 632168SF3 helicase
Domain1009 – 1189181Peptidase C37
Domain1425 – 1546122RdRp catalytic
Nucleotide binding495 – 5028ATP Potential
Compositional bias69 – 735Poly-Pro
Compositional bias944 – 9474Poly-Glu

Sites

Active site10381For 3CLpro activity By similarity
Active site10621For 3CLpro activity By similarity
Active site11471For 3CLpro activity By similarity
Site330 – 3312Cleavage; by 3CLpro By similarity
Site696 – 6972Cleavage; by 3CLpro By similarity
Site875 – 8762Cleavage; by 3CLpro By similarity
Site1008 – 10092Cleavage; by 3CLpro By similarity
Site1189 – 11902Cleavage; by 3CLpro By similarity

Amino acid modifications

Modified residue9021O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

Sequence LengthMass (Da)Tools
P54634 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: FA00B3B67FF3A0B6

FASTA1,699189,201
        10         20         30         40         50         60 
MKMASNDASA AAVVNSNNDT AKSSSDGVLS SMAVTFKRAL GGRAKQPPPR ETPQRPPRPP 

        70         80         90        100        110        120 
TPELVKKIPP PPPNGEDELV VSYSVKDGVS GLPELSTVRQ PDEANTAFSV PPLNQRENRD 

       130        140        150        160        170        180 
AKEPLTGTIL EMWDGEIYHY GLYVERGLVL GVHKPPAAIS LAKVELTPLS LFWRPVYTPQ 

       190        200        210        220        230        240 
YLISPDTLKR LHGESFPYTA FDNNCYAFCC WVLDLNDSWL SRRMIQRTTG FFRPYQDWNR 

       250        260        270        280        290        300 
KPLPTMDDSK LKKVANVFLC ALSSLFTRPI KDIIGKLRPL NILNILASCD WTFAGIVESL 

       310        320        330        340        350        360 
ILLAELFGVF WTPPDVSAMI APLLGDYELQ GPEDLAVELV PIVMGGIGLV LGFTKEKIGK 

       370        380        390        400        410        420 
MLSSAASTLR ACKDLGAYGL EILKLVMKWF FPKKEEANEL AMVRSIEDAV LDLEAIENNH 

       430        440        450        460        470        480 
MTTLLKDKDS LATYMRTLDL EEEKARKLST KSASPDIVGT INALLARIAA ARSLVHRAKE 

       490        500        510        520        530        540 
ELSSRLRPVV VMISGKPGIG KTHLARELAK RIAASLTGDQ RVGLIPRNGV DHWDAYKGER 

       550        560        570        580        590        600 
VVLWDDYGMS NPIHDALRLQ ELADTCPLTL NCDRIENKGK VFDSDAIIIT TNLANPAPLD 

       610        620        630        640        650        660 
YVNFEACSRR IDFLVYAEAP EVEKAKRDFP GQPDMWKNAF SPDFSHIKLA LAPQGGFDKN 

       670        680        690        700        710        720 
GNTPHGKGVM KTLTTGSLIA RASGLLHERL DEYELQGPAL TTFNFDRNKV LAFRQLAAEN 

       730        740        750        760        770        780 
KYGLMDTMKV GRQLKDVRTM PELKQALKNI SIKRCQIVYS GCTYTLESDG KGNVKVDRVQ 

       790        800        810        820        830        840 
SATVQTNHEL AGALHHLRCA RIRYYVKCVQ EALYSIIQIA GAAFVTTRIV KRMNIQDLWS 

       850        860        870        880        890        900 
KPQVEDTEDT ANKDGCPKPK DDEEFVVSSD DIKTEGKKGK NKTGRGKKHT AFSSKGLSDE 

       910        920        930        940        950        960 
EYDEYKRIRE ERNGKYSIEE YLQDRDKYYE EVAIARATEE DFCEEEEAKI RQRIFRPTRK 

       970        980        990       1000       1010       1020 
QRKEERASLG LVTGSEIRKR NPDDFKPKGK LWADDDRSVD YNEKLDFEAP PSIWSRIVNF 

      1030       1040       1050       1060       1070       1080 
GSGWGFWVSP SLFITSTHVI PQGAQEFFGV PVKQIQIHKS GEFCRLRFPK PIRTDVTGMI 

      1090       1100       1110       1120       1130       1140 
LEEGAPEGTV VTLLIKRSTG ELMPLAARMG THATMKIQGR TVGGQMGMLL TGSNAKSMDL 

      1150       1160       1170       1180       1190       1200 
GTTPGDCGCP YIYKRENDYV VIGVHTAAAR GGNTVICATQ GSEGEATLEG GDNKGTYCGA 

      1210       1220       1230       1240       1250       1260 
PILGPGSAPK LSTKTKFWRS STAPLPPGTY EPAYLGGKDP RVKGGPSLQQ VMRDQLKPFT 

      1270       1280       1290       1300       1310       1320 
EPRGKPPKPS VLEAAKRTII NVLEQTIDPP QKWSFTQACA SLDKTTSSGH PHHMRKNDCW 

      1330       1340       1350       1360       1370       1380 
NGESFTGKLA DQASKANLMF EEGKNMTPVY TGALKDELVK TDKIYGKIKK RLLWGSDLAT 

      1390       1400       1410       1420       1430       1440 
MIRCARAFGG LMDELKAHCV TLPIRVGMNM NEDGPIIFER HSRYKYHYDA DYSRWDSTQQ 

      1450       1460       1470       1480       1490       1500 
RAVLAAALEI MVKFSPEPHL AQIVAEDLLS PSVMDVGDFK ISINEGLPSG VPCTSQWNSI 

      1510       1520       1530       1540       1550       1560 
AHWLLTLCAL SEVTNLSPDI IQANSLFSFY GDDEIVSTDI NLNPEKLTAK LKEYGLKPTR 

      1570       1580       1590       1600       1610       1620 
PDKTEGPLII SEDLNGLTFL RRTVTRDPAG WFGKLDQSSI LRQMYWTRGP NHEDPSETMI 

      1630       1640       1650       1660       1670       1680 
PHSQRPIQLM SLLGEAALHG PAFYSKISKL VIAELKEGGM DFYVPRQEPM FRWMRFSDLS 

      1690 
TWEGDRNLAP SFVNEDGVE 

« Hide

References

[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].

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X86557 Genomic RNA. Translation: CAA60254.1.

3D structure databases

ProteinModelPortalP54634.
SMRP54634. Positions 1009-1188, 1195-1695.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSC37.001.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D3.40.50.300. 1 hit.
InterProIPR003593. 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]
PfamPF08405. Calici_PP_N. 1 hit.
PF05416. Peptidase_C37. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSPR00917. SRSVCYSPTASE.
SMARTSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEPS51537. NV_3CL_PRO. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOLG_LORDV
AccessionPrimary (citable) accession number: P54634
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries