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Q8BB16

- REP_PCV2

UniProt

Q8BB16 - REP_PCV2

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Protein

Replication-associated protein

Gene

Rep

Organism
Porcine circovirus 2 (PCV2)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep and/or Rep' binds a specific hairpin at the genome origin of replication. Introduces an endonucleolytic nick within the conserved sequence 5'-AGTATTAC-3' in the intergenic region of the genome, thereby initiating the rolling circle replication (RCR). Following cleavage, binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication. Displays origin-specific DNA cleavage, nucleotidyl transferase, ATPase and helicase activities. ATPase activity is probably carried by the isoform Rep (By similarity).By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Mg2+1 Publication, Mn2+1 PublicationNote: Divalent metal cations, possibly Mg(2+) or Mn(2+).1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi48 – 481Divalent metal cationSequence Analysis
Metal bindingi57 – 571Divalent metal cationSequence Analysis
Active sitei96 – 961For DNA cleavage activityBy similarity
Metal bindingi100 – 1001Divalent metal cationSequence Analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi174 – 1818ATPBy similarity

GO - Molecular functioni

  1. ATPase activity, uncoupled Source: InterPro
  2. ATP binding Source: UniProtKB-KW
  3. DNA binding Source: UniProtKB-KW
  4. endodeoxyribonuclease activity, producing 5'-phosphomonoesters Source: InterPro
  5. metal ion binding Source: UniProtKB-KW
  6. nucleotidyltransferase activity Source: UniProtKB-KW
  7. RNA binding Source: InterPro
  8. RNA helicase activity Source: InterPro

GO - Biological processi

  1. DNA replication Source: UniProtKB-KW
  2. protein-DNA covalent cross-linking Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Helicase, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, DNA-binding, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Replication-associated protein (EC:2.7.7.-, EC:3.1.21.-, EC:3.6.1.3)
Alternative name(s):
ATP-dependent helicase Rep
RepP
Gene namesi
Name:Rep
ORF Names:ORF1
OrganismiPorcine circovirus 2 (PCV2)
Taxonomic identifieri85708 [NCBI]
Taxonomic lineageiVirusesssDNA virusesCircoviridaeCircovirus
Virus hostiSus scrofa (Pig) [TaxID: 9823]
ProteomesiUP000000470: Genome

Subcellular locationi

Host nucleus 1 Publication

GO - Cellular componenti

  1. host cell nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Host nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi179 – 1802GK → DI: Complete loss of viral DNA synthesis. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 314314Replication-associated proteinPRO_0000133089Add
BLAST

Keywords - PTMi

Covalent protein-DNA linkage

Interactioni

Subunit structurei

Interacts with the capsid protein; this interaction relocates Rep into the nucleus.By similarity

Structurei

Secondary structure

1
314
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 114Combined sources
Beta strandi17 – 237Combined sources
Helixi26 – 338Combined sources
Helixi37 – 393Combined sources
Beta strandi40 – 489Combined sources
Beta strandi57 – 6610Combined sources
Helixi70 – 778Combined sources
Turni78 – 803Combined sources
Beta strandi81 – 844Combined sources
Helixi90 – 989Combined sources
Beta strandi103 – 1086Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2HW0NMR-A2-116[»]
ProteinModelPortaliQ8BB16.
SMRiQ8BB16. Positions 2-116.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8BB16.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi4 – 1815Nuclear localization signal1 PublicationAdd
BLAST
Motifi19 – 224RCR-1By similarity
Motifi57 – 626RCR-2By similarity
Motifi96 – 994RCR-3By similarity

Domaini

There are 3 rolling circle replication (RCR) motifs. RCR-2 is probably involved in metal coordination. RCR-3 is required for phosphodiester bond cleavage for initiation of RCR.

Sequence similaritiesi

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR027417. P-loop_NTPase.
IPR003365. Viral_rep_N.
[Graphical view]
PfamiPF00910. RNA_helicase. 1 hit.
PF02407. Viral_Rep. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.

Sequences (10)i

Sequence statusi: Complete.

This entry describes 10 isoformsi produced by alternative promoter usage and alternative splicing. Align

Isoform Rep (identifier: Q8BB16-1) [UniParc]FASTAAdd to Basket

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
MPSKKNGRSG PQPHKRWVFT LNNPSEDERK KIREPPISLF DYFIVGEEGN
60 70 80 90 100
EEGRTPHLQG FANFVKKQTF NKVKWYLGAR CHIEKAKGTD QQNKEYCSKE
110 120 130 140 150
GNLLIECGAP RSQGQRSDLS TAVSTLLESG SLVTVAEQHP VTFVRNFRGL
160 170 180 190 200
AELLKVSGKM QKRDWKTNVH VIVGPPGCGK SKWAANFADP ETTYWKPPRN
210 220 230 240 250
KWWDGYHGEE VVVIDDFYGW LPWDDLLRLC DRYPLTVETK GGTVPFLARS
260 270 280 290 300
ILITSNQTPL EWYSSTAVPA VEALYRRITS LVFWKNATEQ STEEGGQFVT
310
LSPPCPEFPY EINY

Note: Produced by alternative promoter usage.

Length:314
Mass (Da):35,762
Last modified:March 1, 2003 - v1
Checksum:i3FE9D85F2CD656FC
GO
Isoform Rep' (identifier: Q8BB16-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     123-178: VSTLLESGSL...VHVIVGPPGC → YSDYQQSDPV...PVRHPFPPMP
     179-314: Missing.

Note: Produced by alternative splicing of isoform Rep.

Show »
Length:178
Mass (Da):20,240
Checksum:i0D29BACBE4BECDB0
GO
Isoform NS462 (identifier: Q8BB12-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry Q8BB12.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Length:
Mass (Da):
GO
Isoform NS642 (identifier: Q8BB12-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry Q8BB12.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Length:
Mass (Da):
GO
Isoform NS0 (identifier: Q8BB12-1) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry Q8BB12.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by alternative promoter usage.

Length:23
Mass (Da):2,725
GO
Isoform NS515 (identifier: Q8BB16-6)

Sequence is not available

Note: Produced by alternative promoter usage.

Length:
Mass (Da):
Isoform NS672 (identifier: Q8BB16-7)

Sequence is not available

Note: Produced by alternative promoter usage.

Length:
Mass (Da):
Isoform Rep3a (identifier: Q8BB16-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     16-249: Missing.

Note: Produced by alternative splicing of isoform Rep.

Show »
Length:80
Mass (Da):9,003
Checksum:i0116107E943C6EC8
GO
Isoform Rep3b (identifier: Q8BB16-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     16-254: Missing.

Note: Produced by alternative splicing of isoform Rep.

Show »
Length:75
Mass (Da):8,475
Checksum:i4481B5DD3891883E
GO
Isoform Rep3c (identifier: Q8BB16-5)

Sequence is not available

Note: Produced by alternative splicing of isoform Rep.

Length:
Mass (Da):

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei16 – 254239Missing in isoform Rep3b. CuratedVSP_015882Add
BLAST
Alternative sequencei16 – 249234Missing in isoform Rep3a. CuratedVSP_015883Add
BLAST
Alternative sequencei123 – 17856VSTLL…GPPGC → YSDYQQSDPVGMVLLNCCPS CRSSLSEDYFLGILEECYRT IHGGRGPVRHPFPPMP in isoform Rep'. CuratedVSP_015884Add
BLAST
Alternative sequencei179 – 314136Missing in isoform Rep'. CuratedVSP_015885Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY094619 Genomic DNA. Translation: AAM21844.1.
AY094619 Genomic DNA. Translation: AAM21845.1.
AY094619 Genomic DNA. Translation: AAM21846.1.
AY094619 Genomic DNA. Translation: AAM21847.1.

Keywords - Coding sequence diversityi

Alternative promoter usage, Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY094619 Genomic DNA. Translation: AAM21844.1 .
AY094619 Genomic DNA. Translation: AAM21845.1 .
AY094619 Genomic DNA. Translation: AAM21846.1 .
AY094619 Genomic DNA. Translation: AAM21847.1 .

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2HW0 NMR - A 2-116 [» ]
ProteinModelPortali Q8BB16.
SMRi Q8BB16. Positions 2-116.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei Q8BB16.

Family and domain databases

Gene3Di 3.40.50.300. 1 hit.
InterProi IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR027417. P-loop_NTPase.
IPR003365. Viral_rep_N.
[Graphical view ]
Pfami PF00910. RNA_helicase. 1 hit.
PF02407. Viral_Rep. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "Transcriptional analysis of porcine circovirus type 2."
    Cheung A.K.
    Virology 305:168-180(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS REP; REP'; REP3A; REP3B AND REP3C), ALTERNATIVE PROMOTER USAGE.
    Strain: Isolate PCV/688.
  2. "The essential and nonessential transcription units for viral protein synthesis and DNA replication of porcine circovirus type 2."
    Cheung A.K.
    Virology 313:452-459(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF 179-GLY-LYS-180.
    Strain: Isolate PCV/688.
  3. "The N-terminus of porcine circovirus type 2 replication protein is required for nuclear localization and ori binding activities."
    Lin W.-L., Chien M.-S., Du Y.-W., Wu P.-C., Huang C.
    Biochem. Biophys. Res. Commun. 379:1066-1071(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, NUCLEAR LOCALIZATION SIGNAL.
  4. "Solution structure, divalent metal and DNA binding of the endonuclease domain from the replication initiation protein from porcine circovirus 2."
    Vega-Rocha S., Byeon I.-J.L., Gronenborn B., Gronenborn A.M., Campos-Olivas R.
    J. Mol. Biol. 367:473-487(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 1-116, COFACTOR, CHARACTERIZATION.

Entry informationi

Entry nameiREP_PCV2
AccessioniPrimary (citable) accession number: Q8BB16
Secondary accession number(s): Q8BB13, Q8BB14, Q8BB15
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: March 1, 2003
Last modified: November 26, 2014
This is version 61 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, Multifunctional enzyme

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3