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Protein

Capsid scaffolding protein

Gene

BVRF2

Organism
Epstein-Barr virus (strain B95-8) (HHV-4) (Human herpesvirus 4)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Capsid scaffolding protein: Acts as a scaffold protein by binding major capsid protein in the cytoplasm, inducing the nuclear localization of both proteins. Multimerizes in the nucleus such as major capsid protein forms the icosahedral T=16 capsid. Autocatalytic cleavage releases the assembly protein, and subsequently abolishes interaction with major capsid protein. Cleavages products are evicted from the capsid before or during DNA packaging.UniRule annotation1 Publication
Assemblin: Protease that plays an essential role in virion assembly within the nucleus. Catalyzes the cleavage of the assembly protein after formation of the spherical procapsid. By that cleavage, the capsid matures and gains its icosahedral shape. The cleavage sites seem to include -Ala-Ser-, -Ala-Ala-, as well as Ala-Thr bonds. Assemblin and cleavages products are evicted from the capsid before or during DNA packaging.UniRule annotation1 Publication
Assembly protein: Plays a major role in capsid assembly. Acts as a scaffold protein by binding major capsid protein. Multimerizes in the nucleus such as major capsid protein forms the icosahedral T=16 capsid. Cleaved by assemblin after capsid completion. The cleavages products are evicted from the capsid before or during DNA packaging.UniRule annotation1 Publication

Catalytic activityi

Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei48Charge relay systemUniRule annotation1
Active sitei116Charge relay systemUniRule annotation1
Active sitei139Charge relay systemUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Serine protease

Keywords - Biological processi

Viral capsid assembly, Virus exit from host cell

Protein family/group databases

MEROPSiS21.003.

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid scaffolding proteinUniRule annotation
Alternative name(s):
Capsid protein P40
Protease precursorUniRule annotation
Short name:
pPRUniRule annotation
Protein EC-RF3/EC-RF3A
Virion structural protein BVRF2
Cleaved into the following 2 chains:
AssemblinUniRule annotation (EC:3.4.21.97UniRule annotation)
Alternative name(s):
ProteaseUniRule annotation
Assembly proteinUniRule annotation
Alternative name(s):
Capsid assembly proteinUniRule annotation
Gene namesi
ORF Names:BVRF2
OrganismiEpstein-Barr virus (strain B95-8) (HHV-4) (Human herpesvirus 4)
Taxonomic identifieri10377 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageHerpesviralesHerpesviridaeGammaherpesvirinaeLymphocryptovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000007640 Componenti: Genome

Subcellular locationi

Capsid scaffolding protein :
  • Host cytoplasm UniRule annotation
Assemblin :
  • Host nucleus UniRule annotation
Assembly protein :
  • Host nucleus UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Host cytoplasm, Host nucleus

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL4013.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000272791 – 605Capsid scaffolding proteinAdd BLAST605
ChainiPRO_00000272801 – 235AssemblinUniRule annotationAdd BLAST235
ChainiPRO_0000027281236 – 605Assembly proteinUniRule annotationAdd BLAST370

Post-translational modificationi

Capsid scaffolding protein is cleaved by assemblin after formation of the spherical procapsid. As a result, the capsid obtains its mature, icosahedral shape. Cleavages occur at two or more sites: release and tail site.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei235 – 236Cleavage; by assemblin; Release siteUniRule annotation2
Sitei568 – 569Cleavage; by assemblin; Tail siteBy similarity2

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Capsid scaffolding protein homomultimerizes and interacts with major capsid protein. Assemblin exists in a monomer-dimer equilibrium with the dimer being the active species. Assembly protein homomultimerizes and interacts with major capsid protein.UniRule annotation

Chemistry databases

BindingDBiP03234.

Structurei

Secondary structure

1605
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 14Combined sources8
Beta strandi21 – 23Combined sources3
Helixi29 – 35Combined sources7
Beta strandi42 – 46Combined sources5
Beta strandi49 – 62Combined sources14
Beta strandi67 – 73Combined sources7
Helixi76 – 79Combined sources4
Helixi81 – 86Combined sources6
Helixi90 – 93Combined sources4
Helixi103 – 111Combined sources9
Beta strandi114 – 120Combined sources7
Beta strandi136 – 145Combined sources10
Beta strandi147 – 150Combined sources4
Beta strandi154 – 157Combined sources4
Helixi159 – 164Combined sources6
Helixi171 – 184Combined sources14
Helixi198 – 207Combined sources10
Helixi214 – 224Combined sources11
Beta strandi229 – 232Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1O6EX-ray2.30A/B1-235[»]
ProteinModelPortaliP03234.
SMRiP03234.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03234.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni281 – 300Interaction with pAPUniRule annotationAdd BLAST20
Regioni585 – 605Interaction with major capsid proteinUniRule annotationAdd BLAST21

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi410 – 416Nuclear localization signalBy similarity7

Domaini

Region of interaction between pPR and pAP is called Amino conserved domain (ACD). The region of interaction with major capsid protein is called carboxyl conserved domain (CCD).UniRule annotation

Sequence similaritiesi

Belongs to the herpesviridae capsid scaffolding protein family.UniRule annotation

Family and domain databases

HAMAPiMF_04008. HSV_SCAF. 1 hit.
InterProiIPR001847. Peptidase_S21.
[Graphical view]
PfamiPF00716. Peptidase_S21. 1 hit.
[Graphical view]
PRINTSiPR00236. HSVCAPSIDP40.

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative promoter usage. AlignAdd to basket

Isoform Capsid scaffolding protein (identifier: P03234-1) [UniParc]FASTAAdd to basket
Also known as: pPR, EC-RF3

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MVQAPSVYVC GFVERPDAPP KDACLHLDPL TVKSQLPLKK PLPLTVEHLP
60 70 80 90 100
DAPVGSVFGL YQSRAGLFSA ASITSGDFLS LLDSIYHDCD IAQSQRLPLP
110 120 130 140 150
REPKVEALHA WLPSLSLASL HPDIPQTTAD GGKLSFFDHV SICALGRRRG
160 170 180 190 200
TTAVYGTDLA WVLKHFSDLE PSIAAQIEND ANAAKRESGC PEDHPLPLTK
210 220 230 240 250
LIAKAIDAGF LRNRVETLRQ DRGVANIPAE SYLKASDAPD LQKPDKALQS
260 270 280 290 300
PPPASTDPAT MLSGNAGEGA TACGGSAAAG QDLISVPRNT FMTLLQTNLD
310 320 330 340 350
NKPPRQTPLP YAAPLPPFSH QAIATAPSYG PGAGAVAPAG GYFTSPGGYY
360 370 380 390 400
AGPAGGDPGA FLAMDAHTYH PHPHPPPAYF GLPGLFGPPP PVPPYYGSHL
410 420 430 440 450
RADYVPAPSR SNKRKRDPEE DEEGGGLFPG EDATLYRKDI AGLSKSVNEL
460 470 480 490 500
QHTLQALRRE TLSYGHTGVG YCPQQGPCYT HSGPYGFQPH QSYEVPRYVP
510 520 530 540 550
HPPPPPTSHQ AAQAQPPPPG TQAPEAHCVA ESTIPEAGAA GNSGPREDTN
560 570 580 590 600
PQQPTTEGHH RGKKLVQASA SGVAQSKEPT TPKAKSVSAH LKSIFCEELL

NKRVA
Length:605
Mass (Da):64,102
Last modified:July 21, 1986 - v1
Checksum:iFC2D355F8A389708
GO
Isoform pAP (identifier: P03234-2) [UniParc]FASTAAdd to basket
Also known as: Assembly protein, EC-RF3A

The sequence of this isoform differs from the canonical sequence as follows:
     1-260: Missing.

Show »
Length:345
Mass (Da):36,127
Checksum:i33A11158E09C7418
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0188651 – 260Missing in isoform pAP. CuratedAdd BLAST260

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01555 Genomic DNA. Translation: CAA24801.1.
V01555 Genomic DNA. Translation: CAA24802.1.
AJ507799 Genomic DNA. Translation: CAD53454.1.
AJ507799 Genomic DNA. Translation: CAD53455.1.
PIRiA03798. QQBE3R.
RefSeqiYP_401704.1. NC_007605.1.

Genome annotation databases

GeneIDi3783733.
KEGGivg:3783733.

Keywords - Coding sequence diversityi

Alternative promoter usage

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01555 Genomic DNA. Translation: CAA24801.1.
V01555 Genomic DNA. Translation: CAA24802.1.
AJ507799 Genomic DNA. Translation: CAD53454.1.
AJ507799 Genomic DNA. Translation: CAD53455.1.
PIRiA03798. QQBE3R.
RefSeqiYP_401704.1. NC_007605.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1O6EX-ray2.30A/B1-235[»]
ProteinModelPortaliP03234.
SMRiP03234.
ModBaseiSearch...
MobiDBiSearch...

Chemistry databases

BindingDBiP03234.
ChEMBLiCHEMBL4013.

Protein family/group databases

MEROPSiS21.003.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi3783733.
KEGGivg:3783733.

Miscellaneous databases

EvolutionaryTraceiP03234.

Family and domain databases

HAMAPiMF_04008. HSV_SCAF. 1 hit.
InterProiIPR001847. Peptidase_S21.
[Graphical view]
PfamiPF00716. Peptidase_S21. 1 hit.
[Graphical view]
PRINTSiPR00236. HSVCAPSIDP40.
ProtoNetiSearch...

Entry informationi

Entry nameiSCAF_EBVB9
AccessioniPrimary (citable) accession number: P03234
Secondary accession number(s): Q66541, Q777B6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: November 2, 2016
This is version 109 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.