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Q9ICP7

- MREP_SCSVF

UniProt

Q9ICP7 - MREP_SCSVF

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Protein
Master replication protein
Gene
DNA-R, C8
Organism
Subterranean clover stunt virus (strain F) (SCSV)
Status
Reviewed - Annotation score: 4 out of 5 - Protein inferred from homologyi

Functioni

Essential for the replication of all genomic viral ssDNA (trans-replication). The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep binds a specific hairpin at the genome origin of replication. Introduces an endonucleolytic nick within the conserved sequence 5'-A[GT]TATTAC-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 By similarity.

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Divalent metal cations, possibly magnesium or manganese By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi33 – 331Divalent metal cation Reviewed prediction
Metal bindingi41 – 411Divalent metal cation Reviewed prediction
Active sitei79 – 791For DNA cleavage activity By similarity
Metal bindingi84 – 841Divalent metal cation Reviewed prediction

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi180 – 1889ATP By similarity

GO - Molecular functioni

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

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:
Master replication protein (EC:2.7.7.-, EC:3.1.21.-, EC:3.6.1.3)
Short name:
M-Rep
Gene namesi
Name:DNA-R
Synonyms:C8
OrganismiSubterranean clover stunt virus (strain F) (SCSV)
Taxonomic identifieri291607 [NCBI]
Taxonomic lineageiVirusesssDNA virusesNanoviridaeNanovirus
Virus hostiMedicago arabica [TaxID: 70936]
Medicago lupulina [TaxID: 47085]
Medicago minima [TaxID: 70957]
Phaseolus vulgaris (Kidney bean) (French bean) [TaxID: 3885]
Pisum sativum (Garden pea) [TaxID: 3888]
Trifolium cernuum [TaxID: 74509]
Trifolium dubium (Suckling clover) (Lesser trefoil) [TaxID: 97021]
Trifolium glomeratum [TaxID: 74514]
Trifolium pratense (Red clover) [TaxID: 57577]
Trifolium repens (Creeping white clover) [TaxID: 3899]
Trifolium subterraneum (Subterranean clover) [TaxID: 3900]
Vicia faba (Broad bean) (Faba vulgaris) [TaxID: 3906]
Wisteria sinensis [TaxID: 20997]
ProteomesiUP000006543: Genome

Subcellular locationi

Host nucleus Reviewed prediction

GO - Cellular componenti

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

Keywords - Cellular componenti

Host nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 286286Master replication protein
PRO_0000378521Add
BLAST

Keywords - PTMi

Covalent protein-DNA linkage

Interactioni

Subunit structurei

Homooligomer Reviewed prediction. Rep binds to repeated DNA motifs (iterons) By similarity.

Structurei

3D structure databases

ProteinModelPortaliQ9ICP7.
SMRiQ9ICP7. Positions 2-95.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi10 – 134RCR-1 By similarity
Motifi41 – 466RCR-2 By similarity
Motifi50 – 7021Nuclear localization signal Reviewed prediction
Add
BLAST
Motifi79 – 824RCR-3 By similarity
Motifi96 – 1027Nuclear localization signal Reviewed prediction

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 By similarity.

Sequence similaritiesi

Family and domain databases

InterProiIPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR003365. Viral_rep_N.
[Graphical view]
PfamiPF00910. RNA_helicase. 1 hit.
PF02407. Viral_Rep. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9ICP7-1 [UniParc]FASTAAdd to Basket

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MARQVICWCF TLNNPLAPLS LHESMKYLVY QTEAGDNGTI HYQGYVEMKK    50
RTSLVQMKKL LPGAHLEKRR GSQGEARAYA MKEDSRVEGP WEFGEFKEVL 100
EDKLRSVMED MKSTGKRPVE YIEDCCNTYD KSSATLREFR GELKKKQAIE 150
EWQLQRQPWM DEVERLMETK DCRRIIWVYG PQGGEGKTSY AKHLVKTRDA 200
FYSTGGKTAD IAFAWDHQEL VLFDFPRSFE EYVNYGVIEQ LKNGIVQSGK 250
YQSIVKYCNY VEVIVFANFI PRSGMFSEDR IVIVYA 286
Length:286
Mass (Da):33,281
Last modified:October 1, 2000 - v1
Checksum:i3E49185793F09C58
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AJ290434 Genomic DNA. Translation: CAB96405.1.
RefSeqiNP_620694.1. NC_003812.1.

Genome annotation databases

GeneIDi991157.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AJ290434 Genomic DNA. Translation: CAB96405.1 .
RefSeqi NP_620694.1. NC_003812.1.

3D structure databases

ProteinModelPortali Q9ICP7.
SMRi Q9ICP7. Positions 2-95.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 991157.

Family and domain databases

InterProi IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR003365. Viral_rep_N.
[Graphical view ]
Pfami PF00910. RNA_helicase. 1 hit.
PF02407. Viral_Rep. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "The master rep concept in nanovirus replication: identification of missing genome components and potential for natural genetic reassortment."
    Timchenko T., Katul L., Sano Y., de Kouchkovsky F., Vetten H.J., Gronenborn B.
    Virology 274:189-195(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

Entry informationi

Entry nameiMREP_SCSVF
AccessioniPrimary (citable) accession number: Q9ICP7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 7, 2009
Last sequence update: October 1, 2000
Last modified: April 16, 2014
This is version 40 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

The genome of nanoviruses is composed of six to eight segments. In addition, some isolates contain subviral DNAs.

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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