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Protein

DNA primase small subunit

Gene

PRIM1

Organism
Homo sapiens (Human)
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.

Sites

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

GO - Molecular functioni

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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication, Transcription

Keywords - Ligandi

Metal-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

HGNCiHGNC:9369. PRIM1.

Subcellular locationi

GO - Cellular componenti

  • alpha DNA polymerase:primase complex Source: GO_Central
  • membrane Source: UniProtKB
  • nucleoplasm Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Primosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi5557.
OpenTargetsiENSG00000198056.
PharmGKBiPA33739.

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.

PTM databases

iPTMnetiP49642.
PhosphoSitePlusiP49642.

Expressioni

Gene expression databases

BgeeiENSG00000198056.
CleanExiHS_PRIM1.
ExpressionAtlasiP49642. baseline and differential.
GenevisibleiP49642. HS.

Organism-specific databases

HPAiHPA040010.

Interactioni

Subunit structurei

Heterodimer of a small subunit and a large subunit.

Protein-protein interaction databases

BioGridi111547. 28 interactors.
IntActiP49642. 5 interactors.
MINTiMINT-234425.
STRINGi9606.ENSP00000350491.

Structurei

Secondary structure

1420
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 8Combined sources3
Helixi9 – 19Combined sources11
Helixi23 – 30Combined sources8
Helixi32 – 34Combined sources3
Turni37 – 42Combined sources6
Beta strandi43 – 48Combined sources6
Helixi50 – 52Combined sources3
Beta strandi54 – 58Combined sources5
Helixi63 – 73Combined sources11
Beta strandi76 – 86Combined sources11
Helixi88 – 93Combined sources6
Turni96 – 98Combined sources3
Beta strandi101 – 103Combined sources3
Beta strandi106 – 111Combined sources6
Helixi112 – 118Combined sources7
Beta strandi120 – 122Combined sources3
Turni129 – 132Combined sources4
Helixi133 – 148Combined sources16
Beta strandi155 – 159Combined sources5
Beta strandi161 – 169Combined sources9
Helixi172 – 175Combined sources4
Helixi179 – 189Combined sources11
Helixi210 – 219Combined sources10
Turni220 – 222Combined sources3
Helixi223 – 227Combined sources5
Turni228 – 230Combined sources3
Helixi237 – 244Combined sources8
Helixi249 – 251Combined sources3
Helixi252 – 261Combined sources10
Helixi265 – 275Combined sources11
Beta strandi282 – 284Combined sources3
Helixi293 – 301Combined sources9
Helixi307 – 311Combined sources5
Turni325 – 327Combined sources3
Helixi336 – 341Combined sources6
Helixi344 – 346Combined sources3
Helixi350 – 360Combined sources11
Beta strandi380 – 382Combined sources3
Helixi383 – 385Combined sources3
Helixi389 – 406Combined sources18

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...

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.
OMAiHAYNPEV.
OrthoDBiEOG091G0EAF.
PhylomeDBiP49642.
TreeFamiTF312823.

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.

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

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0218985D → A.Corresponds to variant rs2277339dbSNPEnsembl.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

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. 28 interactors.
IntActiP49642. 5 interactors.
MINTiMINT-234425.
STRINGi9606.ENSP00000350491.

PTM databases

iPTMnetiP49642.
PhosphoSitePlusiP49642.

Polymorphism and mutation databases

BioMutaiPRIM1.
DMDMi1346792.

Proteomic databases

EPDiP49642.
MaxQBiP49642.
PaxDbiP49642.
PeptideAtlasiP49642.
PRIDEiP49642.

Protocols and materials databases

DNASUi5557.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi5557.
DisGeNETi5557.
GeneCardsiPRIM1.
HGNCiHGNC:9369. PRIM1.
HPAiHPA040010.
MIMi176635. gene.
neXtProtiNX_P49642.
OpenTargetsiENSG00000198056.
PharmGKBiPA33739.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2851. Eukaryota.
COG1467. LUCA.
GeneTreeiENSGT00390000011466.
HOGENOMiHOG000196041.
HOVERGENiHBG003006.
InParanoidiP49642.
KOiK02684.
OMAiHAYNPEV.
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.
PROiP49642.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000198056.
CleanExiHS_PRIM1.
ExpressionAtlasiP49642. baseline and differential.
GenevisibleiP49642. HS.

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_HUMAN
AccessioniPrimary (citable) accession number: P49642
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: November 30, 2016
This is version 156 of the entry and version 1 of the sequence. [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

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  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. SIMILARITY comments
    Index of protein domains and families

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.