P54634 (POLG_LORDV) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Lordsdale virus (strain GII/Human/United Kingdom/Lordsdale/1993) (Human enteric calicivirus) (Hu/NV/LD/1993/UK) [Complete proteome]

Taxonomic identifier

82658 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Norovirus › Norwalk virus › Norovirus genogroup II

Virus host

Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	1699 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred 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 encodes 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.

Ontologies

Keywords
Biological process	Host-virus interaction Viral RNA replication
Ligand	ATP-binding Nucleotide-binding
Molecular function	Hydrolase Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase
PTM	Covalent protein-RNA linkage Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	RNA-protein covalent cross-linking Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral genome replication Inferred from electronic annotation. Source: InterPro virus-host interaction Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro RNA helicase activity Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1699	1699	Genome polyprotein		PRO_0000341998
	Chain	1 – 330	330	Protein p37		PRO_0000036914
	Chain	331 – 696	366	NTPase		PRO_0000036915
	Chain	697 – 875	179	Protein p20		PRO_0000036916
	Chain	876 – 1007	132	Viral genome-linked protein		PRO_0000036917
	Chain	1008 – 1189	182	3C-like protease		PRO_0000036918
	Chain	1190 – 1699	510	RNA-directed RNA polymerase		PRO_0000036919
Regions
	Domain	465 – 632	168	SF3 helicase
	Domain	1009 – 1189	181	Peptidase C37
	Domain	1425 – 1546	122	RdRp catalytic
	Nucleotide binding	495 – 502	8	ATP Potential
	Compositional bias	69 – 73	5	Poly-Pro
	Compositional bias	944 – 947	4	Poly-Glu
Sites
	Active site	1038	1	For 3CLpro activity By similarity
	Active site	1062	1	For 3CLpro activity By similarity
	Active site	1147	1	For 3CLpro activity By similarity
	Site	330 – 331	2	Cleavage; by 3CLpro By similarity
	Site	696 – 697	2	Cleavage; by 3CLpro By similarity
	Site	875 – 876	2	Cleavage; by 3CLpro By similarity
	Site	1008 – 1009	2	Cleavage; by 3CLpro By similarity
	Site	1189 – 1190	2	Cleavage; by 3CLpro By similarity
Amino acid modifications
	Modified residue	902	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	P54634 [UniParc]. Last modified October 1, 1996. Version 1. Checksum: FA00B3B67FF3A0B6	FASTA	1,699	189,201
	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

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
ProteinModelPortal	P54634.
SMR	P54634. Positions 1009-1188, 1195-1695.
ModBase	Search...
Protein family/group databases
MEROPS	C37.001.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR003593. AAA+_ATPase. IPR000605. Helicase_SF3_ssDNA/RNA_vir. IPR014759. Helicase_SF3_ssRNA_vir. IPR001665. Norovirus_pept_C37. IPR001205. RNA-dir_pol_C. IPR007094. RNA-dir_pol_PSvirus. IPR009003. Trypsin-like_Pept_dom. IPR013614. Viral_PP_Calicivir_N. [Graphical view]
Pfam	PF08405. Calici_PP_N. 1 hit. PF05416. Peptidase_C37. 1 hit. PF00680. RdRP_1. 1 hit. PF00910. RNA_helicase. 1 hit. [Graphical view]
PRINTS	PR00917. SRSVCYSPTASE.
SMART	SM00382. AAA. 1 hit. [Graphical view]
SUPFAM	SSF50494. Pept_Ser_Cys. 1 hit.
PROSITE	PS51537. NV_3CL_PRO. 1 hit. PS50507. RDRP_SSRNA_POS. 1 hit. PS51218. SF3_HELICASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLG_LORDV

Accession

Primary (citable) accession number: P54634

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	May 1, 2013
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program