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Protein

DNA primase small subunit

Gene

PRI1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. In a complex with DNA polymerase alpha (DNA polymerase alpha:primase) constitutes a replicative polymerase. Both primase components participate in formation of the active center, but the ATP-binding site is exclusively located on p48.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei46Sequence analysis1
Active sitei111Sequence analysis1
Active sitei113Sequence analysis1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • DNA primase activity Source: SGD
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • DNA replication Source: SGD
  • DNA replication, synthesis of RNA primer Source: SGD
  • DNA replication initiation Source: SGD
  • lagging strand elongation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication, Transcription

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-31429-MONOMER.
ReactomeiR-SCE-113501. Inhibition of replication initiation of damaged DNA by RB1/E2F1.
R-SCE-174411. Polymerase switching on the C-strand of the telomere.
R-SCE-174430. Telomere C-strand synthesis initiation.
R-SCE-68952. DNA replication initiation.
R-SCE-68962. Activation of the pre-replicative complex.
R-SCE-69091. Polymerase switching.
R-SCE-69166. Removal of the Flap Intermediate.
R-SCE-69183. Processive synthesis on the lagging strand.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA primase small subunit (EC:2.7.7.-)
Alternative name(s):
DNA polymerase alpha:primase complex p48 subunit
Short name:
DNA polymerase-primase complex p48 subunit
Short name:
Pol alpha-primase complex p48 subunit
DNA primase 48 kDa subunit
Gene namesi
Name:PRI1
Ordered Locus Names:YIR008C
ORF Names:YIB8C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IX

Organism-specific databases

EuPathDBiFungiDB:YIR008C.
SGDiS000001447. PRI1.

Subcellular locationi

GO - Cellular componenti

  • alpha DNA polymerase:primase complex Source: SGD
  • nuclear replication fork Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Primosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi184R → Q: Temperature-sensitive. 1 Publication1
Mutagenesisi316E → K: Cold-sensitive. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000467361 – 409DNA primase small subunitAdd BLAST409

Proteomic databases

MaxQBiP10363.
PRIDEiP10363.

PTM databases

iPTMnetiP10363.

Interactioni

Subunit structurei

DNA polymerase alpha:primase is a four subunit enzyme complex, which is assembled throughout the cell cycle, and consists of the two DNA polymerase subunits A and B, and the DNA primase large and small subunits.

Protein-protein interaction databases

BioGridi35000. 148 interactors.
DIPiDIP-2534N.
IntActiP10363. 6 interactors.
MINTiMINT-572443.

Structurei

Secondary structure

1409
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi12 – 21Combined sources10
Helixi25 – 33Combined sources9
Beta strandi34 – 37Combined sources4
Helixi40 – 43Combined sources4
Beta strandi45 – 50Combined sources6
Beta strandi56 – 60Combined sources5
Helixi65 – 75Combined sources11
Beta strandi78 – 88Combined sources11
Helixi90 – 92Combined sources3
Beta strandi103 – 105Combined sources3
Beta strandi108 – 113Combined sources6
Helixi114 – 117Combined sources4
Turni118 – 120Combined sources3
Helixi131 – 150Combined sources20
Beta strandi157 – 161Combined sources5
Beta strandi163 – 171Combined sources9
Helixi174 – 177Combined sources4
Helixi181 – 191Combined sources11
Beta strandi199 – 201Combined sources3
Helixi211 – 220Combined sources10
Helixi221 – 223Combined sources3
Helixi224 – 227Combined sources4
Helixi228 – 232Combined sources5
Helixi238 – 244Combined sources7
Helixi246 – 248Combined sources3
Helixi252 – 264Combined sources13
Helixi270 – 285Combined sources16
Beta strandi287 – 289Combined sources3
Helixi290 – 309Combined sources20
Helixi315 – 319Combined sources5
Turni333 – 335Combined sources3
Helixi348 – 350Combined sources3
Helixi354 – 363Combined sources10
Helixi367 – 369Combined sources3
Helixi373 – 401Combined sources29

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LIMX-ray1.63A8-396[»]
4MM2X-ray1.60A/B1-409[»]
ProteinModelPortaliP10363.
SMRiP10363.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi123 – 133Zinc knuckle motifAdd BLAST11

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000011466.
HOGENOMiHOG000196041.
InParanoidiP10363.
KOiK02684.
OMAiFGFKHIM.
OrthoDBiEOG092C20OL.

Family and domain databases

CDDicd04860. AE_Prim_S. 1 hit.
InterProiIPR002755. DNA_primase_S.
IPR014052. DNA_primase_ssu_euk/arc.
[Graphical view]
PANTHERiPTHR10536. PTHR10536. 1 hit.
PfamiPF01896. DNA_primase_S. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00335. primase_sml. 1 hit.

Sequencei

Sequence statusi: Complete.

P10363-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTNSVKTNGP SSSDMEYYYK SLYPFKHIFN WLNHSPKPSR DMINREFAMA
60 70 80 90 100
FRSGAYKRYN SFNSVQDFKA QIEKANPDRF EIGAIYNKPP RERDTLLKSE
110 120 130 140 150
LKALEKELVF DIDMDDYDAF RTCCSGAQVC SKCWKFISLA MKITNTALRE
160 170 180 190 200
DFGYKDFIWV FSGRRGAHCW VSDKRARALT DVQRRNVLDY VNVIRDRNTD
210 220 230 240 250
KRLALKRPYH PHLARSLEQL KPFFVSIMLE EQNPWEDDQH AIQTLLPALY
260 270 280 290 300
DKQLIDSLKK YWLDNPRRSS KEKWNDIDQI ATSLFKGPKQ DSHIIKLREC
310 320 330 340 350
KEDLVLMTLY PKLDVEVTKQ TIHLLKAPFC IHPATGNVCV PIDESFAPEK
360 370 380 390 400
APKLIDLQTE MEKNNDVSLT ALQPFINQFQ AYVSSLLKNE LGSVKRERED

DDEPASLDF
Length:409
Mass (Da):47,690
Last modified:February 1, 1995 - v2
Checksum:iC4B1C82257AA86F2
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti231 – 232EQ → DE in CAA68513 (PubMed:3313275).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z37996 Genomic DNA. Translation: CAA86078.1.
X79743 Genomic DNA. Translation: CAB38098.1.
Y00458 Genomic DNA. Translation: CAA68513.1.
AY692859 Genomic DNA. Translation: AAT92878.1.
BK006942 Genomic DNA. Translation: DAA08554.1.
PIRiS48352.
RefSeqiNP_012273.1. NM_001179530.1.

Genome annotation databases

EnsemblFungiiYIR008C; YIR008C; YIR008C.
GeneIDi854825.
KEGGisce:YIR008C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z37996 Genomic DNA. Translation: CAA86078.1.
X79743 Genomic DNA. Translation: CAB38098.1.
Y00458 Genomic DNA. Translation: CAA68513.1.
AY692859 Genomic DNA. Translation: AAT92878.1.
BK006942 Genomic DNA. Translation: DAA08554.1.
PIRiS48352.
RefSeqiNP_012273.1. NM_001179530.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LIMX-ray1.63A8-396[»]
4MM2X-ray1.60A/B1-409[»]
ProteinModelPortaliP10363.
SMRiP10363.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35000. 148 interactors.
DIPiDIP-2534N.
IntActiP10363. 6 interactors.
MINTiMINT-572443.

PTM databases

iPTMnetiP10363.

Proteomic databases

MaxQBiP10363.
PRIDEiP10363.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYIR008C; YIR008C; YIR008C.
GeneIDi854825.
KEGGisce:YIR008C.

Organism-specific databases

EuPathDBiFungiDB:YIR008C.
SGDiS000001447. PRI1.

Phylogenomic databases

GeneTreeiENSGT00390000011466.
HOGENOMiHOG000196041.
InParanoidiP10363.
KOiK02684.
OMAiFGFKHIM.
OrthoDBiEOG092C20OL.

Enzyme and pathway databases

BioCyciYEAST:G3O-31429-MONOMER.
ReactomeiR-SCE-113501. Inhibition of replication initiation of damaged DNA by RB1/E2F1.
R-SCE-174411. Polymerase switching on the C-strand of the telomere.
R-SCE-174430. Telomere C-strand synthesis initiation.
R-SCE-68952. DNA replication initiation.
R-SCE-68962. Activation of the pre-replicative complex.
R-SCE-69091. Polymerase switching.
R-SCE-69166. Removal of the Flap Intermediate.
R-SCE-69183. Processive synthesis on the lagging strand.

Miscellaneous databases

PROiP10363.

Family and domain databases

CDDicd04860. AE_Prim_S. 1 hit.
InterProiIPR002755. DNA_primase_S.
IPR014052. DNA_primase_ssu_euk/arc.
[Graphical view]
PANTHERiPTHR10536. PTHR10536. 1 hit.
PfamiPF01896. DNA_primase_S. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00335. primase_sml. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPRI1_YEAST
AccessioniPrimary (citable) accession number: P10363
Secondary accession number(s): D6VVT8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: February 1, 1995
Last modified: November 30, 2016
This is version 154 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

The bound zinc ion is not a cofactor. It is bound to a zinc knuckle motif that may be involved in sequence recognition and the binding of ssDNA (By similarity).By similarity
Present with 197 molecules/cell in log phase SD medium.1 Publication

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
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome IX
    Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

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.