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Protein

Capsid scaffolding protein

Gene

33

Organism
Varicella-zoster virus (strain Dumas) (HHV-3) (Human herpesvirus 3)
Status
Reviewed-Annotation score: Annotation score: 4 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 annotation
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 annotation
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 annotation

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei52Charge relay systemUniRule annotation1
Active sitei120Charge relay systemUniRule annotation1
Active sitei139Charge relay systemUniRule annotation1

GO - Molecular functioni

GO - Biological processi

  • nuclear capsid assembly Source: UniProtKB
  • viral release from host cell Source: UniProtKB-KW
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

MEROPSiS21.005.

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid scaffolding proteinUniRule annotation
Alternative name(s):
Protease precursorUniRule annotation
Short name:
pPRUniRule annotation
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
Name:33
OrganismiVaricella-zoster virus (strain Dumas) (HHV-3) (Human herpesvirus 3)
Taxonomic identifieri10338 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageHerpesviralesHerpesviridaeAlphaherpesvirinaeVaricellovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000002602 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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000272691 – 605Capsid scaffolding proteinAdd BLAST605
ChainiPRO_00000272701 – 236AssemblinUniRule annotationAdd BLAST236
ChainiPRO_0000027271237 – 605Assembly proteinUniRule annotationAdd BLAST369

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
Sitei236 – 237Cleavage; by assemblin; Release siteUniRule annotation2
Sitei578 – 579Cleavage; by assemblin; Tail siteBy similarity2

Keywords - PTMi

Phosphoprotein

Proteomic databases

PRIDEiP09286.

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

Structurei

Secondary structure

1605
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi13 – 19Combined sources7
Turni22 – 25Combined sources4
Turni27 – 29Combined sources3
Helixi33 – 39Combined sources7
Beta strandi47 – 50Combined sources4
Beta strandi57 – 66Combined sources10
Beta strandi68 – 77Combined sources10
Helixi80 – 89Combined sources10
Helixi97 – 100Combined sources4
Helixi106 – 115Combined sources10
Beta strandi118 – 122Combined sources5
Beta strandi139 – 145Combined sources7
Beta strandi154 – 158Combined sources5
Helixi159 – 162Combined sources4
Beta strandi167 – 169Combined sources3
Helixi171 – 183Combined sources13
Helixi195 – 207Combined sources13
Turni208 – 211Combined sources4
Helixi215 – 226Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VZVX-ray3.00A11-231[»]
ProteinModelPortaliP09286.
SMRiP09286.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP09286.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni326 – 344Interaction with pAPUniRule annotationAdd BLAST19
Regioni585 – 605Interaction with major capsid proteinUniRule annotationAdd BLAST21

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: P09286-1) [UniParc]FASTAAdd to basket
Also known as: pPR

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
MAAEADEENC EALYVAGYLA LYSKDEGELN ITPEIVRSAL PPTSKIPINI
60 70 80 90 100
DHRKDCVVGE VIAIIEDIRG PFFLGIVRCP QLHAVLFEAA HSNFFGNRDS
110 120 130 140 150
VLSPLERALY LVTNYLPSVS LSSKRLSPNE IPDGNFFTHV ALCVVGRRVG
160 170 180 190 200
TVVNYDCTPE SSIEPFRVLS MESKARLLSL VKDYAGLNKV WKVSEDKLAK
210 220 230 240 250
VLLSTAVNNM LLRDRWDVVA KRRREAGIMG HVYLQASTGY GLARITNVNG
260 270 280 290 300
VESKLPNAGV INATFHPGGP IYDLALGVGE SNEDCEKTVP HLKVTQLCRN
310 320 330 340 350
DSDMASVAGN ASNISPQPPS GVPTGGEFVL IPTAYYSQLL TGQTKNPQVS
360 370 380 390 400
IGAPNNGQYI VGPYGSPHPP AFPPNTGGYG CPPGHFGGPY GFPGYPPPNR
410 420 430 440 450
LEMQMSAFMN ALAAERGIDL QTPCVNFPDK TDVRRPGKRD FKSMDQRELD
460 470 480 490 500
SFYSGESQMD GEFPSNIYFP GEPTYITHRR RRVSPSYWQR RHRVSNGQHE
510 520 530 540 550
ELAGVVAKLQ QEVTELKSQN GTQMPLSHHT NIPEGTRDPR ISILLKQLQS
560 570 580 590 600
VSGLCSSQNT TSTPHTDTVG QDVNAVEASS KAPLIQGSTA DDADMFANQM

MVGRC
Length:605
Mass (Da):66,047
Last modified:July 1, 1989 - v1
Checksum:i2F2C2FE6AB6D2C17
GO
Isoform pAP (identifier: P09286-2) [UniParc]FASTAAdd to basket
Also known as: Assembly protein

The sequence of this isoform differs from the canonical sequence as follows:
     1-303: Missing.

Show »
Length:302
Mass (Da):32,767
Checksum:i768CC28FCABC906E
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0374201 – 303Missing in isoform pAP. CuratedAdd BLAST303

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04370 Genomic DNA. Translation: CAA27916.1.
X04370 Genomic DNA. Translation: CAH19069.1.
PIRiG27214. WZBE33.

Keywords - Coding sequence diversityi

Alternative promoter usage

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04370 Genomic DNA. Translation: CAA27916.1.
X04370 Genomic DNA. Translation: CAH19069.1.
PIRiG27214. WZBE33.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VZVX-ray3.00A11-231[»]
ProteinModelPortaliP09286.
SMRiP09286.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiS21.005.

Proteomic databases

PRIDEiP09286.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP09286.

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_VZVD
AccessioniPrimary (citable) accession number: P09286
Secondary accession number(s): Q65ZF9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: November 30, 2016
This is version 98 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.