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Protein

DNA primase large subunit

Gene

PRIM2

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.

Cofactori

[4Fe-4S] cluster1 PublicationNote: Binds 1 [4Fe-4S] cluster.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi287Iron-sulfur (4Fe-4S)1
Metal bindingi367Iron-sulfur (4Fe-4S)1
Metal bindingi384Iron-sulfur (4Fe-4S)1
Metal bindingi424Iron-sulfur (4Fe-4S)1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Nucleotidyltransferase, Transferase
Biological processDNA replication, Transcription
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding

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 large subunit (EC:2.7.7.-)
Alternative name(s):
DNA primase 58 kDa subunit
Short name:
p58
Gene namesi
Name:PRIM2
Synonyms:PRIM2A
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000146143.17
HGNCiHGNC:9370 PRIM2
MIMi176636 gene
neXtProtiNX_P49643

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

DisGeNETi5558
OpenTargetsiENSG00000146143
PharmGKBiPA162400108

Chemistry databases

ChEMBLiCHEMBL2363042

Polymorphism and mutation databases

DMDMi51338777

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000467681 – 509DNA primase large subunitAdd BLAST509

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei470PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP49643
MaxQBiP49643
PeptideAtlasiP49643
PRIDEiP49643
ProteomicsDBi56041
56042 [P49643-2]

PTM databases

iPTMnetiP49643
PhosphoSitePlusiP49643

Expressioni

Gene expression databases

BgeeiENSG00000146143
CleanExiHS_PRIM2
ExpressionAtlasiP49643 baseline and differential
GenevisibleiP49643 HS

Organism-specific databases

HPAiHPA046566

Interactioni

Subunit structurei

Heterodimer of a small subunit and a large subunit.

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi111548, 28 interactors
ComplexPortaliCPX-2087 DNA polymerase alpha:primase complex
CORUMiP49643
DIPiDIP-36438N
IntActiP49643, 18 interactors
MINTiP49643

Structurei

Secondary structure

1509
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi39 – 61Combined sources23
Helixi67 – 80Combined sources14
Helixi90 – 92Combined sources3
Helixi96 – 110Combined sources15
Helixi114 – 134Combined sources21
Helixi137 – 145Combined sources9
Beta strandi146 – 148Combined sources3
Helixi156 – 169Combined sources14
Beta strandi170 – 172Combined sources3
Beta strandi179 – 181Combined sources3
Beta strandi183 – 187Combined sources5
Helixi188 – 191Combined sources4
Helixi192 – 195Combined sources4
Turni196 – 198Combined sources3
Beta strandi200 – 210Combined sources11
Helixi211 – 235Combined sources25
Helixi238 – 241Combined sources4
Turni245 – 250Combined sources6
Turni252 – 255Combined sources4
Helixi273 – 276Combined sources4
Helixi277 – 283Combined sources7
Helixi286 – 298Combined sources13
Helixi303 – 316Combined sources14
Beta strandi318 – 324Combined sources7
Turni333 – 335Combined sources3
Helixi338 – 343Combined sources6
Beta strandi345 – 351Combined sources7
Beta strandi355 – 357Combined sources3
Helixi367 – 372Combined sources6
Helixi385 – 388Combined sources4
Helixi391 – 400Combined sources10
Helixi405 – 416Combined sources12
Helixi420 – 432Combined sources13
Helixi444 – 455Combined sources12

3D structure databases

ProteinModelPortaliP49643
SMRiP49643
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP49643

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000009790
HOGENOMiHOG000212154
HOVERGENiHBG008257
InParanoidiP49643
KOiK02685
OMAiDCHGCPY
OrthoDBiEOG091G08G7
PhylomeDBiP49643

Family and domain databases

CDDicd07322 PriL_PriS_Eukaryotic, 1 hit
InterProiView protein in InterPro
IPR016558 DNA_primase_lsu_euk
IPR007238 DNA_primase_lsu_euk/arc
PANTHERiPTHR10537 PTHR10537, 1 hit
PfamiView protein in Pfam
PF04104 DNA_primase_lrg, 1 hit
PIRSFiPIRSF009449 DNA_primase_large_subunit, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P49643-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MEFSGRKWRK LRLAGDQRNA SYPHCLQFYL QPPSENISLI EFENLAIDRV
60 70 80 90 100
KLLKSVENLG VSYVKGTEQY QSKLESELRK LKFSYRENLE DEYEPRRRDH
110 120 130 140 150
ISHFILRLAY CQSEELRRWF IQQEMDLLRF RFSILPKDKI QDFLKDSQLQ
160 170 180 190 200
FEAISDEEKT LREQEIVASS PSLSGLKLGF ESIYKIPFAD ALDLFRGRKV
210 220 230 240 250
YLEDGFAYVP LKDIVAIILN EFRAKLSKAL ALTARSLPAV QSDERLQPLL
260 270 280 290 300
NHLSHSYTGQ DYSTQGNVGK ISLDQIDLLS TKSFPPCMRQ LHKALRENHH
310 320 330 340 350
LRHGGRMQYG LFLKGIGLTL EQALQFWKQE FIKGKMDPDK FDKGYSYNIR
360 370 380 390 400
HSFGKEGKRT DYTPFSCLKI ILSNPPSQGD YHGCPFRHSD PELLKQKLQS
410 420 430 440 450
YKISPGGISQ ILDLVKGTHY QVACQKYFEM IHNVDDCGFS LNHPNQFFCE
460 470 480 490 500
SQRILNGGKD IKKEPIQPET PQPKPSVQKT KDASSALASL NSSLEMDMEG

LEDYFSEDS
Length:509
Mass (Da):58,806
Last modified:August 16, 2004 - v2
Checksum:i80195D48103F87A7
GO
Isoform 2 (identifier: P49643-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     154-158: ISDEE → VSIFL
     159-509: Missing.

Note: No experimental confirmation available.
Show »
Length:158
Mass (Da):19,144
Checksum:iBF57630E126F1D14
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti8W → R in CAA52378 (PubMed:8026492).Curated1
Sequence conflicti40I → T in CAA52378 (PubMed:8026492).Curated1
Sequence conflicti88N → K in CAA52378 (PubMed:8026492).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_059742181E → K. Corresponds to variant dbSNP:rs5011403Ensembl.1
Natural variantiVAR_059743204D → G. Corresponds to variant dbSNP:rs6913546Ensembl.1
Natural variantiVAR_059744259G → S. Corresponds to variant dbSNP:rs927192Ensembl.1
Natural variantiVAR_051506265Q → L. Corresponds to variant dbSNP:rs3763183Ensembl.1
Natural variantiVAR_059745287C → Y. Corresponds to variant dbSNP:rs9476080Ensembl.1
Natural variantiVAR_059747446Q → H. Corresponds to variant dbSNP:rs4294007Ensembl.1
Natural variantiVAR_059748465P → SCombined sourcesCorresponds to variant dbSNP:rs4294008Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_015111154 – 158ISDEE → VSIFL in isoform 2. 1 Publication5
Alternative sequenceiVSP_015112159 – 509Missing in isoform 2. 1 PublicationAdd BLAST351

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X74331 mRNA Translation: CAA52378.1
AL121975 Genomic DNA No translation available.
AL162579 Genomic DNA No translation available.
BC017833 mRNA Translation: AAH17833.1
BC064931 mRNA Translation: AAH64931.1
CCDSiCCDS75476.1 [P49643-1]
CCDS75477.1 [P49643-2]
PIRiS45631
RefSeqiNP_000938.2, NM_000947.4 [P49643-1]
NP_001269416.1, NM_001282487.1 [P49643-2]
NP_001269417.1, NM_001282488.1 [P49643-2]
UniGeneiHs.654580

Genome annotation databases

EnsembliENST00000274891; ENSP00000485304; ENSG00000146143 [P49643-2]
ENST00000370687; ENSP00000483201; ENSG00000146143 [P49643-2]
ENST00000615550; ENSP00000484105; ENSG00000146143 [P49643-1]
GeneIDi5558
KEGGihsa:5558
UCSCiuc003pdv.3 human [P49643-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiPRI2_HUMAN
AccessioniPrimary (citable) accession number: P49643
Secondary accession number(s): Q53FJ8
, Q6P1Q7, Q8WVL2, Q9H413
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: August 16, 2004
Last modified: July 18, 2018
This is version 160 of the entry and version 2 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. Human chromosome 6
    Human chromosome 6: 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

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