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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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei44 – 441Sequence analysis
Active sitei109 – 1091Sequence analysis
Active sitei111 – 1111Sequence analysis

GO - Molecular functioni

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

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-69109. Leading Strand Synthesis.
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

  • membrane Source: UniProtKB
  • nucleoplasm Source: Reactome
  • primosome complex Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Primosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33739.

Polymorphism and mutation databases

BioMutaiPRIM1.
DMDMi1346792.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 420420DNA primase small subunitPRO_0000046730Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineCombined sources

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP49642.
MaxQBiP49642.
PaxDbiP49642.
PRIDEiP49642.

PTM databases

iPTMnetiP49642.
PhosphoSiteiP49642.

Expressioni

Gene expression databases

BgeeiP49642.
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 interactions.
IntActiP49642. 5 interactions.
MINTiMINT-234425.
STRINGi9606.ENSP00000350491.

Structurei

Secondary structure

1
420
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 83Combined sources
Helixi9 – 1911Combined sources
Helixi23 – 308Combined sources
Helixi32 – 343Combined sources
Turni37 – 426Combined sources
Beta strandi43 – 486Combined sources
Helixi50 – 523Combined sources
Beta strandi54 – 585Combined sources
Helixi63 – 7311Combined sources
Beta strandi76 – 8611Combined sources
Helixi88 – 936Combined sources
Turni96 – 983Combined sources
Beta strandi101 – 1033Combined sources
Beta strandi106 – 1116Combined sources
Helixi112 – 1187Combined sources
Beta strandi120 – 1223Combined sources
Turni129 – 1324Combined sources
Helixi133 – 14816Combined sources
Beta strandi155 – 1595Combined sources
Beta strandi161 – 1699Combined sources
Helixi172 – 1754Combined sources
Helixi179 – 18911Combined sources
Helixi210 – 21910Combined sources
Turni220 – 2223Combined sources
Helixi223 – 2275Combined sources
Turni228 – 2303Combined sources
Helixi237 – 2448Combined sources
Helixi249 – 2513Combined sources
Helixi252 – 26110Combined sources
Helixi265 – 27511Combined sources
Beta strandi282 – 2843Combined sources
Helixi293 – 3019Combined sources
Helixi307 – 3115Combined sources
Turni325 – 3273Combined sources
Helixi336 – 3416Combined sources
Helixi344 – 3463Combined sources
Helixi350 – 36011Combined sources
Beta strandi380 – 3823Combined sources
Helixi383 – 3853Combined sources
Helixi389 – 40618Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-419.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi121 – 13111Zinc knuckle motifAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2851. Eukaryota.
COG1467. LUCA.
GeneTreeiENSGT00390000011466.
HOGENOMiHOG000196041.
HOVERGENiHBG003006.
InParanoidiP49642.
KOiK02684.
OMAiQYTYPRI.
OrthoDBiEOG74TWZW.
PhylomeDBiP49642.
TreeFamiTF312823.

Family and domain databases

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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti5 – 51D → A.
Corresponds to variant rs2277339 [ dbSNP | Ensembl ].
VAR_021898

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
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. Positions 1-419.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiP49642.
PhosphoSiteiP49642.

Polymorphism and mutation databases

BioMutaiPRIM1.
DMDMi1346792.

Proteomic databases

EPDiP49642.
MaxQBiP49642.
PaxDbiP49642.
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.
GeneCardsiPRIM1.
HGNCiHGNC:9369. PRIM1.
HPAiHPA040010.
MIMi176635. gene.
neXtProtiNX_P49642.
PharmGKBiPA33739.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2851. Eukaryota.
COG1467. LUCA.
GeneTreeiENSGT00390000011466.
HOGENOMiHOG000196041.
HOVERGENiHBG003006.
InParanoidiP49642.
KOiK02684.
OMAiQYTYPRI.
OrthoDBiEOG74TWZW.
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-69109. Leading Strand Synthesis.
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

BgeeiP49642.
CleanExiHS_PRIM1.
ExpressionAtlasiP49642. baseline and differential.
GenevisibleiP49642. HS.

Family and domain databases

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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Bone marrow.
  3. "Mapping of the human DNA primase 1 (PRIM1) to chromosome 12q13."
    Cloutier S., Hamel H., Champagne M., Yotov W.V.
    Genomics 43:398-401(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] OF 97-146.
  4. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  5. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

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: June 8, 2016
This is version 151 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.