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Protein

DNA primase small subunit

Gene

PRIM1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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.

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei44Sequence analysis1
Active sitei109Sequence analysis1
Active sitei111Sequence analysis1

GO - Molecular functioni

  • DNA primase activity Source: GO_Central
  • metal ion binding Source: UniProtKB-KW
  • single-stranded DNA binding Source: GO_Central

GO - Biological processi

Keywordsi

Molecular functionNucleotidyltransferase, Transferase
Biological processDNA replication, Transcription
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-113501 Inhibition of replication initiation of damaged DNA by RB1/E2F1
R-HSA-174411 Polymerase switching on the C-strand of the telomere
R-HSA-174430 Telomere C-strand synthesis initiation
R-HSA-68952 DNA replication initiation
R-HSA-68962 Activation of the pre-replicative complex
R-HSA-69091 Polymerase switching
R-HSA-69166 Removal of the Flap Intermediate
R-HSA-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 primase 49 kDa subunit
Short name:
p49
Gene namesi
Name:PRIM1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

EuPathDBiHostDB:ENSG00000198056.13
HGNCiHGNC:9369 PRIM1
MIMi176635 gene
neXtProtiNX_P49642

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

DNA-directed RNA polymerase, Primosome

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000198056
PharmGKBiPA33739

Chemistry databases

ChEMBLiCHEMBL2363042

Polymorphism and mutation databases

BioMutaiPRIM1
DMDMi1346792

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000467301 – 420DNA primase small subunitAdd BLAST420

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP49642
MaxQBiP49642
PaxDbiP49642
PeptideAtlasiP49642
PRIDEiP49642
ProteomicsDBi56040

PTM databases

iPTMnetiP49642
PhosphoSitePlusiP49642

Expressioni

Gene expression databases

BgeeiENSG00000198056 Expressed in 169 organ(s), highest expression level in female gonad
CleanExiHS_PRIM1
ExpressionAtlasiP49642 baseline and differential
GenevisibleiP49642 HS

Organism-specific databases

HPAiHPA040010

Interactioni

Subunit structurei

Heterodimer of a small subunit and a large subunit.

Binary interactionsi

WithEntry#Exp.IntActNotes
PRIM2P496434EBI-726050,EBI-850004

Protein-protein interaction databases

BioGridi111547, 31 interactors
ComplexPortaliCPX-2087 DNA polymerase alpha:primase complex
CORUMiP49642
IntActiP49642, 12 interactors
STRINGi9606.ENSP00000350491

Structurei

Secondary structure

1420
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP49642
SMRiP49642
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi121 – 131Zinc knuckle motifAdd BLAST11

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2851 Eukaryota
COG1467 LUCA
GeneTreeiENSGT00390000011466
HOGENOMiHOG000196041
HOVERGENiHBG003006
InParanoidiP49642
KOiK02684
OMAiVYYRRLF
OrthoDBiEOG091G0EAF
PhylomeDBiP49642
TreeFamiTF312823

Family and domain databases

CDDicd04860 AE_Prim_S, 1 hit
InterProiView protein in InterPro
IPR002755 DNA_primase_S
IPR014052 DNA_primase_ssu_euk/arc
PANTHERiPTHR10536 PTHR10536, 1 hit
PfamiView protein in Pfam
PF01896 DNA_primase_S, 1 hit
TIGRFAMsiTIGR00335 primase_sml, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 3 potential isoforms that are computationally mapped.Show allAlign All

P49642-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
METFDPTELP ELLKLYYRRL FPYSQYYRWL NYGGVIKNYF QHREFSFTLK
60 70 80 90 100
DDIYIRYQSF NNQSDLEKEM QKMNPYKIDI GAVYSHRPNQ HNTVKLGAFQ
110 120 130 140 150
AQEKELVFDI DMTDYDDVRR CCSSADICPK CWTLMTMAIR IIDRALKEDF
160 170 180 190 200
GFKHRLWVYS GRRGVHCWVC DESVRKLSSA VRSGIVEYLS LVKGGQDVKK
210 220 230 240 250
KVHLSEKIHP FIRKSINIIK KYFEEYALVN QDILENKESW DKILALVPET
260 270 280 290 300
IHDELQQSFQ KSHNSLQRWE HLKKVASRYQ NNIKNDKYGP WLEWEIMLQY
310 320 330 340 350
CFPRLDINVS KGINHLLKSP FSVHPKTGRI SVPIDLQKVD QFDPFTVPTI
360 370 380 390 400
SFICRELDAI STNEEEKEEN EAESDVKHRT RDYKKTSLAP YVKVFEHFLE
410 420
NLDKSRKGEL LKKSDLQKDF
Length:420
Mass (Da):49,902
Last modified:February 1, 1996 - v1
Checksum:i9B5AC900E0C3CCE8
GO

Computationally mapped potential isoform sequencesi

There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F8VNY2F8VNY2_HUMAN
DNA primase
PRIM1
327Annotation score:
F8VSB2F8VSB2_HUMAN
DNA primase small subunit
PRIM1
185Annotation score:
H0YIP2H0YIP2_HUMAN
DNA primase small subunit
PRIM1
152Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0218985D → A. Corresponds to variant dbSNP:rs2277339Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X74330 mRNA Translation: CAA52377.1
BC005266 mRNA Translation: AAH05266.1
U89689 Genomic DNA Translation: AAC51726.1
CCDSiCCDS44926.1
PIRiS45630
RefSeqiNP_000937.1, NM_000946.2
UniGeneiHs.534339

Genome annotation databases

EnsembliENST00000338193; ENSP00000350491; ENSG00000198056
GeneIDi5557
KEGGihsa:5557
UCSCiuc001smd.4 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X74330 mRNA Translation: CAA52377.1
BC005266 mRNA Translation: AAH05266.1
U89689 Genomic DNA Translation: AAC51726.1
CCDSiCCDS44926.1
PIRiS45630
RefSeqiNP_000937.1, NM_000946.2
UniGeneiHs.534339

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4BPUX-ray2.70A/C1-420[»]
4BPWX-ray3.00A/C1-420[»]
4BPXX-ray3.40A/C1-420[»]
4LIKX-ray1.70A1-408[»]
4LILX-ray2.60A1-408[»]
4MHQX-ray2.20A1-420[»]
4RR2X-ray2.65A/C1-420[»]
5EXRX-ray3.60A/E1-420[»]
ProteinModelPortaliP49642
SMRiP49642
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111547, 31 interactors
ComplexPortaliCPX-2087 DNA polymerase alpha:primase complex
CORUMiP49642
IntActiP49642, 12 interactors
STRINGi9606.ENSP00000350491

Chemistry databases

ChEMBLiCHEMBL2363042

PTM databases

iPTMnetiP49642
PhosphoSitePlusiP49642

Polymorphism and mutation databases

BioMutaiPRIM1
DMDMi1346792

Proteomic databases

EPDiP49642
MaxQBiP49642
PaxDbiP49642
PeptideAtlasiP49642
PRIDEiP49642
ProteomicsDBi56040

Protocols and materials databases

DNASUi5557
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000338193; ENSP00000350491; ENSG00000198056
GeneIDi5557
KEGGihsa:5557
UCSCiuc001smd.4 human

Organism-specific databases

CTDi5557
EuPathDBiHostDB:ENSG00000198056.13
GeneCardsiPRIM1
HGNCiHGNC:9369 PRIM1
HPAiHPA040010
MIMi176635 gene
neXtProtiNX_P49642
OpenTargetsiENSG00000198056
PharmGKBiPA33739
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2851 Eukaryota
COG1467 LUCA
GeneTreeiENSGT00390000011466
HOGENOMiHOG000196041
HOVERGENiHBG003006
InParanoidiP49642
KOiK02684
OMAiVYYRRLF
OrthoDBiEOG091G0EAF
PhylomeDBiP49642
TreeFamiTF312823

Enzyme and pathway databases

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

Miscellaneous databases

ChiTaRSiPRIM1 human
GenomeRNAii5557
PROiPR:P49642
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000198056 Expressed in 169 organ(s), highest expression level in female gonad
CleanExiHS_PRIM1
ExpressionAtlasiP49642 baseline and differential
GenevisibleiP49642 HS

Family and domain databases

CDDicd04860 AE_Prim_S, 1 hit
InterProiView protein in InterPro
IPR002755 DNA_primase_S
IPR014052 DNA_primase_ssu_euk/arc
PANTHERiPTHR10536 PTHR10536, 1 hit
PfamiView protein in Pfam
PF01896 DNA_primase_S, 1 hit
TIGRFAMsiTIGR00335 primase_sml, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPRI1_HUMAN
AccessioniPrimary (citable) accession number: P49642
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: November 7, 2018
This is version 168 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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