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Protein

Gag polyprotein

Gene

gag

Organism
Human spumaretrovirus (SFVcpz(hu)) (Human foamy virus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in capsid formation and genome binding. Shortly after infection, interaction between incoming particle-associated Gag proteins and host dynein allows centrosomal targeting of the viral genome (associated to Gag), prior to nucleus translocation and integration into host genome.2 Publications

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, RNA-binding, Viral nucleoprotein
Biological processCytoplasmic inwards viral transport, Host-virus interaction, Microtubular inwards viral transport, Viral budding, Viral budding via the host ESCRT complexes, Virus entry into host cell, Virus exit from host cell

Enzyme and pathway databases

BRENDAi3.4.23.B11. 2705.

Names & Taxonomyi

Protein namesi
Recommended name:
Gag polyprotein
Alternative name(s):
Pr71Gag
Cleaved into the following 2 chains:
Alternative name(s):
p68Gag
Alternative name(s):
p3Gag
Gene namesi
Name:gag
OrganismiHuman spumaretrovirus (SFVcpz(hu)) (Human foamy virus)
Taxonomic identifieri11963 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeSpumaretrovirinaeSpumavirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000138352 Componenti: Genome

Subcellular locationi

Gag protein :
  • Virion
  • Host nucleus
  • Host cytoplasm

  • Note: Nuclear at initial phase, cytoplasmic at assembly. Shortly after infection, Gag protein is targeted to centrosomes. It is then actively transported into the nucleus thanks to its nuclear localization signal. In the late phases of infection, Gag proteins assemble in the cytoplasm to form the virion's capsids.

GO - Cellular componenti

  • host cell cytoplasm Source: UniProtKB-SubCell
  • host cell nucleus Source: UniProtKB-SubCell
  • host cytoskeleton Source: CACAO
  • viral nucleocapsid Source: UniProtKB-KW

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Host nucleus, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi17L → A: No effect on capsid export. Reduced virus titer. 1 Publication1
Mutagenesisi17L → S: Complete loss of capsid egress from transfected cells. 1 Publication1
Mutagenesisi44W → A: 75% loss of particle export. Reduced virus titer. 1 Publication1
Mutagenesisi45W → A: Complete loss of capsid egress from transfected cells. 1 Publication1
Mutagenesisi50R → A: Complete loss of capsid egress from transfected cells. 1 Publication1
Mutagenesisi56L → A: Complete loss of capsid egress from transfected cells. 1 Publication1
Mutagenesisi58L → A: Complete loss of capsid egress from transfected cells. 1 Publication1
Mutagenesisi65P → A: 75% loss of particle export. 1 Publication1
Mutagenesisi171L → G: Drastically reduces infectivity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001254751 – 648Gag polyproteinAdd BLAST648
ChainiPRO_00002454371 – 621Gag proteinAdd BLAST621
ChainiPRO_0000245438622 – 648p3Add BLAST27

Post-translational modificationi

Specific enzymatic cleavages in vivo by viral protease yield mature proteins. The protease is not cleaved off from Pol. Since cleavage efficiency is not optimal for all sites, intermediary molecules are expressed.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei311 – 312Cleavage; by viral protease; low efficiencySequence analysis2
Sitei339 – 340Cleavage; by viral protease; low efficiencySequence analysis2
Sitei352 – 353Cleavage; by viral protease; low efficiencySequence analysis2
Sitei621 – 622Cleavage; by viral protease; partial2

Interactioni

Subunit structurei

Gag protein specifically interacts with the N-terminus of leader peptide (By similarity). This specific interaction between Gag protein and Env glycoprotein may compensate for the lack of a Gag membrane targeting signal, and allow particle egress. The capsid is composed of multimeric Gag protein. Interacts with human TSG101. Interacts with host light chain cytoplasmic dynein DYNLL1; this interaction is critical for intracellular microtubule-dependent viral genome transport toward the centrosome.By similarity2 Publications

Structurei

Secondary structure

1648
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 12Combined sources3
Helixi14 – 23Combined sources10
Beta strandi35 – 41Combined sources7
Beta strandi46 – 48Combined sources3
Beta strandi50 – 59Combined sources10
Beta strandi65 – 73Combined sources9
Beta strandi83 – 88Combined sources6
Helixi90 – 93Combined sources4
Turni94 – 96Combined sources3
Helixi105 – 112Combined sources8
Helixi122 – 126Combined sources5
Helixi132 – 135Combined sources4
Helixi140 – 177Combined sources38
Helixi308 – 314Combined sources7
Turni321 – 323Combined sources3
Helixi324 – 338Combined sources15
Helixi344 – 355Combined sources12
Turni365 – 367Combined sources3
Helixi371 – 382Combined sources12
Beta strandi384 – 386Combined sources3
Beta strandi387 – 389Combined sources3
Helixi393 – 401Combined sources9
Helixi404 – 415Combined sources12
Helixi419 – 426Combined sources8
Turni427 – 429Combined sources3
Beta strandi430 – 432Combined sources3
Helixi433 – 445Combined sources13
Beta strandi446 – 448Combined sources3
Helixi450 – 454Combined sources5
Helixi456 – 467Combined sources12
Beta strandi470 – 473Combined sources4
Beta strandi475 – 477Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4JNHX-ray2.40A/B1-179[»]
5M1GNMR-A/B381-477[»]
5M1HNMR-A300-477[»]
SMRiP14349.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni37 – 60Involved in viral assembly and exportSequence analysisAdd BLAST24
Regioni485 – 510Nucleic acid-binding; GR-box 1Add BLAST26
Regioni535 – 556GR-box 2Add BLAST22
Regioni586 – 618GR-box 3Add BLAST33

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi284 – 287PTAP/PSAP motif4
Motifi535 – 556Nuclear localization signal1 PublicationAdd BLAST22

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi188 – 325Pro-richAdd BLAST138
Compositional biasi485 – 510Arg/Gly-richAdd BLAST26
Compositional biasi500 – 609Gln-richAdd BLAST110
Compositional biasi535 – 556Arg/Gly-richAdd BLAST22
Compositional biasi586 – 618Arg/Gly-richAdd BLAST33

Domaini

Gag protein contains 3 glycine-arginine motifs (GR-boxes) necessary for RNA packaging, the first of which has nucleic acid binding properties in vitro.
Late-budding 'domains' (L domains) are short sequence motifs essential for viral particle budding. They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins. Nucleocapsid protein p14 contains one L domain: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101.

Phylogenomic databases

OrthoDBiVOG0900009E.

Family and domain databases

InterProiView protein in InterPro
IPR004957. Gag.
PfamiView protein in Pfam
PF03276. Gag_spuma. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P14349-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASGSNVEEY ELDVEALVVI LRDRNIPRNP LHGEVIGLRL TEGWWGQIER
60 70 80 90 100
FQMVRLILQD DDNEPLQRPR YEVIQRAVNP HTMFMISGPL AELQLAFQDL
110 120 130 140 150
DLPEGPLRFG PLANGHYVQG DPYSSSYRPV TMAETAQMTR DELEDVLNTQ
160 170 180 190 200
SEIEIQMINL LELYEVETRA LRRQLAERSS TGQGGISPGA PRSRPPVSSF
210 220 230 240 250
SGLPSLPSIP GIHPRAPSPP RATSTPGNIP WSLGDDSPPS SSFPGPSQPR
260 270 280 290 300
VSFHPGNPFV EEEGHRPRSQ SRERRREILP APVPSAPPMI QYIPVPPPPP
310 320 330 340 350
IGTVIPIQHI RSVTGEPPRN PREIPIWLGR NAPAIDGVFP VTTPDLRCRI
360 370 380 390 400
INAILGGNIG LSLTPGDCLT WDSAVATLFI RTHGTFPMHQ LGNVIKGIVD
410 420 430 440 450
QEGVATAYTL GMMLSGQNYQ LVSGIIRGYL PGQAVVTALQ QRLDQEIDNQ
460 470 480 490 500
TRAETFIQHL NAVYEILGLN ARGQSIRASV TPQPRPSRGR GRGQNTSRPS
510 520 530 540 550
QGPANSGRGR QRPASGQSNR GSSTQNQNQD NLNQGGYNLR PRTYQPQRYG
560 570 580 590 600
GGRGRRWNDN TNNQESRPSD QGSQTPRPNQ AGSGVRGNQS QTPRPAAGRG
610 620 630 640
GRGNHNRNQR SSGAGDSRAV NTVTQSATSS TDESSSAVTA ASGGDQRD
Length:648
Mass (Da):70,591
Last modified:July 11, 2006 - v2
Checksum:iC7ECBC8B96E77109
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M19427 Genomic RNA. Translation: AAA66555.1. Different termination.
U21247 Genomic RNA. Translation: AAB48111.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M19427 Genomic RNA. Translation: AAA66555.1. Different termination.
U21247 Genomic RNA. Translation: AAB48111.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4JNHX-ray2.40A/B1-179[»]
5M1GNMR-A/B381-477[»]
5M1HNMR-A300-477[»]
SMRiP14349.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

OrthoDBiVOG0900009E.

Enzyme and pathway databases

BRENDAi3.4.23.B11. 2705.

Family and domain databases

InterProiView protein in InterPro
IPR004957. Gag.
PfamiView protein in Pfam
PF03276. Gag_spuma. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiGAG_FOAMV
AccessioniPrimary (citable) accession number: P14349
Secondary accession number(s): P89871
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: July 11, 2006
Last modified: March 15, 2017
This is version 94 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

Foamy viruses are distinct from other retroviruses in many respects. Their protease is active as an uncleaved Pro-Pol protein. Mature particles do not include the usual processed retroviral structural protein (MA, CA and NC), but instead contain two large Gag proteins. Their functional nucleic acid appears to be either RNA or dsDNA (up to 20% of extracellular particles), because they probably proceed either to an early (before integration) or late reverse transcription (after assembly). Foamy viruses have the ability to retrotranspose intracellularly with high efficiency. They bud predominantly into the endoplasmic reticulum (ER) and occasionally at the plasma membrane. Budding requires the presence of Env proteins. Most viral particles probably remain within the infected cell.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

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.