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P49643

- PRI2_HUMAN

UniProt

P49643 - PRI2_HUMAN

Protein

DNA primase large subunit

Gene

PRIM2

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 125 (01 Oct 2014)
      Sequence version 2 (16 Aug 2004)
      Previous versions | rss
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    Functioni

    DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication.

    Cofactori

    Binds 1 4Fe-4S cluster.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi287 – 2871Iron-sulfur (4Fe-4S)
    Metal bindingi367 – 3671Iron-sulfur (4Fe-4S)
    Metal bindingi384 – 3841Iron-sulfur (4Fe-4S)
    Metal bindingi424 – 4241Iron-sulfur (4Fe-4S)

    GO - Molecular functioni

    1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
    2. DNA binding Source: UniProtKB-KW
    3. DNA primase activity Source: ProtInc
    4. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. DNA replication, synthesis of RNA primer Source: ProtInc
    2. DNA replication initiation Source: Reactome
    3. DNA strand elongation involved in DNA replication Source: Reactome
    4. G1/S transition of mitotic cell cycle Source: Reactome
    5. mitotic cell cycle Source: Reactome
    6. telomere maintenance Source: Reactome
    7. telomere maintenance via recombination Source: Reactome
    8. telomere maintenance via semi-conservative replication Source: Reactome

    Keywords - Molecular functioni

    Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    DNA replication, Transcription

    Keywords - Ligandi

    4Fe-4S, DNA-binding, Iron, Iron-sulfur, Metal-binding

    Enzyme and pathway databases

    ReactomeiREACT_1095. Activation of the pre-replicative complex.
    REACT_1385. Processive synthesis on the lagging strand.
    REACT_1792. Polymerase switching.
    REACT_1838. Leading Strand Synthesis.
    REACT_2244. DNA replication initiation.
    REACT_329. Inhibition of replication initiation of damaged DNA by RB1/E2F1.
    REACT_70. Removal of the Flap Intermediate.
    REACT_7987. Polymerase switching on the C-strand of the telomere.
    REACT_7993. Telomere C-strand synthesis initiation.

    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
    ProteomesiUP000005640: Unplaced

    Organism-specific databases

    HGNCiHGNC:9370. PRIM2.

    Subcellular locationi

    GO - Cellular componenti

    1. nucleoplasm Source: Reactome
    2. primosome complex Source: UniProtKB-KW

    Keywords - Cellular componenti

    DNA-directed RNA polymerase, Primosome

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA162400108.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 509509DNA primase large subunitPRO_0000046768Add
    BLAST

    Proteomic databases

    MaxQBiP49643.
    PaxDbiP49643.
    PRIDEiP49643.

    PTM databases

    PhosphoSiteiP49643.

    Expressioni

    Gene expression databases

    CleanExiHS_PRIM2.
    GenevestigatoriP49643.

    Interactioni

    Subunit structurei

    Heterodimer of a small subunit and a large subunit.

    Protein-protein interaction databases

    BioGridi111548. 11 interactions.
    DIPiDIP-36438N.
    IntActiP49643. 7 interactions.
    MINTiMINT-3017566.
    STRINGi9606.ENSP00000402620.

    Structurei

    Secondary structure

    1
    509
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi39 – 6123
    Helixi68 – 8013
    Helixi96 – 10914
    Helixi114 – 13320
    Helixi137 – 1459
    Turni146 – 1483
    Helixi156 – 1594
    Helixi163 – 1697
    Beta strandi179 – 1813
    Beta strandi183 – 1875
    Helixi188 – 1914
    Helixi192 – 1954
    Turni196 – 1983
    Beta strandi200 – 2034
    Beta strandi206 – 2105
    Helixi211 – 23525
    Helixi240 – 2423
    Helixi244 – 2463
    Turni247 – 2515
    Helixi273 – 2764
    Helixi277 – 2837
    Helixi286 – 29813
    Helixi303 – 31614
    Beta strandi318 – 3247
    Turni333 – 3353
    Helixi338 – 3447
    Beta strandi345 – 3517
    Helixi367 – 3726
    Helixi385 – 3884
    Helixi391 – 40010
    Helixi405 – 41612
    Helixi420 – 43213
    Helixi444 – 45512

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3L9QX-ray1.70A/B272-464[»]
    3Q36X-ray2.50A/B266-457[»]
    4BPUX-ray2.70B/D1-253[»]
    4BPWX-ray3.00B/D1-253[»]
    4BPXX-ray3.40B/D19-253[»]
    ProteinModelPortaliP49643.
    SMRiP49643. Positions 29-253, 271-455.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP49643.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG2219.
    HOGENOMiHOG000212154.
    HOVERGENiHBG008257.
    InParanoidiP49643.
    KOiK02685.
    PhylomeDBiP49643.

    Family and domain databases

    InterProiIPR016558. DNA_primase_lsu_euk.
    IPR007238. DNA_primase_lsu_euk/arc.
    [Graphical view]
    PfamiPF04104. DNA_primase_lrg. 1 hit.
    [Graphical view]
    PIRSFiPIRSF009449. DNA_primase_large_subunit. 1 hit.

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    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

    MEFSGRKWRK LRLAGDQRNA SYPHCLQFYL QPPSENISLI EFENLAIDRV    50
    KLLKSVENLG VSYVKGTEQY QSKLESELRK LKFSYRENLE DEYEPRRRDH 100
    ISHFILRLAY CQSEELRRWF IQQEMDLLRF RFSILPKDKI QDFLKDSQLQ 150
    FEAISDEEKT LREQEIVASS PSLSGLKLGF ESIYKIPFAD ALDLFRGRKV 200
    YLEDGFAYVP LKDIVAIILN EFRAKLSKAL ALTARSLPAV QSDERLQPLL 250
    NHLSHSYTGQ DYSTQGNVGK ISLDQIDLLS TKSFPPCMRQ LHKALRENHH 300
    LRHGGRMQYG LFLKGIGLTL EQALQFWKQE FIKGKMDPDK FDKGYSYNIR 350
    HSFGKEGKRT DYTPFSCLKI ILSNPPSQGD YHGCPFRHSD PELLKQKLQS 400
    YKISPGGISQ ILDLVKGTHY QVACQKYFEM IHNVDDCGFS LNHPNQFFCE 450
    SQRILNGGKD IKKEPIQPET PQPKPSVQKT KDASSALASL NSSLEMDMEG 500
    LEDYFSEDS 509
    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)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti8 – 81W → R in CAA52378. (PubMed:8026492)Curated
    Sequence conflicti40 – 401I → T in CAA52378. (PubMed:8026492)Curated
    Sequence conflicti88 – 881N → K in CAA52378. (PubMed:8026492)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti181 – 1811E → K.
    Corresponds to variant rs5011403 [ dbSNP | Ensembl ].
    VAR_059742
    Natural varianti204 – 2041D → G.
    Corresponds to variant rs6913546 [ dbSNP | Ensembl ].
    VAR_059743
    Natural varianti259 – 2591G → S.
    Corresponds to variant rs927192 [ dbSNP | Ensembl ].
    VAR_059744
    Natural varianti265 – 2651Q → L.
    Corresponds to variant rs3763183 [ dbSNP | Ensembl ].
    VAR_051506
    Natural varianti287 – 2871C → Y.
    Corresponds to variant rs9476080 [ dbSNP | Ensembl ].
    VAR_059745
    Natural varianti435 – 4351D → G.
    Corresponds to variant rs4307164 [ dbSNP | Ensembl ].
    VAR_059746
    Natural varianti446 – 4461Q → H.
    Corresponds to variant rs4294007 [ dbSNP | Ensembl ].
    VAR_059747
    Natural varianti465 – 4651P → S.1 Publication
    Corresponds to variant rs4294008 [ dbSNP | Ensembl ].
    VAR_059748

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei154 – 1585ISDEE → VSIFL in isoform 2. 1 PublicationVSP_015111
    Alternative sequencei159 – 509351Missing in isoform 2. 1 PublicationVSP_015112Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X74331 mRNA. Translation: CAA52378.1.
    AL121975, AL162579 Genomic DNA. Translation: CAI20534.1.
    AL162579, AL121975 Genomic DNA. Translation: CAH73686.1.
    BC017833 mRNA. Translation: AAH17833.1.
    BC064931 mRNA. Translation: AAH64931.1.
    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

    GeneIDi5558.
    KEGGihsa:5558.
    UCSCiuc003pdv.1. human. [P49643-2]
    uc003pdx.3. human. [P49643-1]

    Polymorphism databases

    DMDMi51338777.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X74331 mRNA. Translation: CAA52378.1 .
    AL121975 , AL162579 Genomic DNA. Translation: CAI20534.1 .
    AL162579 , AL121975 Genomic DNA. Translation: CAH73686.1 .
    BC017833 mRNA. Translation: AAH17833.1 .
    BC064931 mRNA. Translation: AAH64931.1 .
    PIRi S45631.
    RefSeqi NP_000938.2. NM_000947.4. [P49643-1 ]
    NP_001269416.1. NM_001282487.1. [P49643-2 ]
    NP_001269417.1. NM_001282488.1. [P49643-2 ]
    UniGenei Hs.654580.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3L9Q X-ray 1.70 A/B 272-464 [» ]
    3Q36 X-ray 2.50 A/B 266-457 [» ]
    4BPU X-ray 2.70 B/D 1-253 [» ]
    4BPW X-ray 3.00 B/D 1-253 [» ]
    4BPX X-ray 3.40 B/D 19-253 [» ]
    ProteinModelPortali P49643.
    SMRi P49643. Positions 29-253, 271-455.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 111548. 11 interactions.
    DIPi DIP-36438N.
    IntActi P49643. 7 interactions.
    MINTi MINT-3017566.
    STRINGi 9606.ENSP00000402620.

    PTM databases

    PhosphoSitei P49643.

    Polymorphism databases

    DMDMi 51338777.

    Proteomic databases

    MaxQBi P49643.
    PaxDbi P49643.
    PRIDEi P49643.

    Protocols and materials databases

    DNASUi 5558.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 5558.
    KEGGi hsa:5558.
    UCSCi uc003pdv.1. human. [P49643-2 ]
    uc003pdx.3. human. [P49643-1 ]

    Organism-specific databases

    CTDi 5558.
    GeneCardsi GC06P057179.
    HGNCi HGNC:9370. PRIM2.
    MIMi 176636. gene.
    neXtProti NX_P49643.
    PharmGKBi PA162400108.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG2219.
    HOGENOMi HOG000212154.
    HOVERGENi HBG008257.
    InParanoidi P49643.
    KOi K02685.
    PhylomeDBi P49643.

    Enzyme and pathway databases

    Reactomei REACT_1095. Activation of the pre-replicative complex.
    REACT_1385. Processive synthesis on the lagging strand.
    REACT_1792. Polymerase switching.
    REACT_1838. Leading Strand Synthesis.
    REACT_2244. DNA replication initiation.
    REACT_329. Inhibition of replication initiation of damaged DNA by RB1/E2F1.
    REACT_70. Removal of the Flap Intermediate.
    REACT_7987. Polymerase switching on the C-strand of the telomere.
    REACT_7993. Telomere C-strand synthesis initiation.

    Miscellaneous databases

    EvolutionaryTracei P49643.
    GeneWikii PRIM2.
    GenomeRNAii 5558.
    NextBioi 21538.
    PROi P49643.
    SOURCEi Search...

    Gene expression databases

    CleanExi HS_PRIM2.
    Genevestigatori P49643.

    Family and domain databases

    InterProi IPR016558. DNA_primase_lsu_euk.
    IPR007238. DNA_primase_lsu_euk/arc.
    [Graphical view ]
    Pfami PF04104. DNA_primase_lrg. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF009449. DNA_primase_large_subunit. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    2. "The DNA sequence and analysis of human chromosome 6."
      Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
      , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
      Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. "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] (ISOFORMS 1 AND 2).
      Tissue: Skin.
    4. "An iron-sulfur cluster in the C-terminal domain of the p58 subunit of human DNA primase."
      Weiner B.E., Huang H., Dattilo B.M., Nilges M.J., Fanning E., Chazin W.J.
      J. Biol. Chem. 282:33444-33451(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: IRON-SULFUR CLUSTER, COFACTOR.
    5. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    6. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
      Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
      Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
      Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
      Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. Cited for: VARIANT [LARGE SCALE ANALYSIS] SER-465, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiPRI2_HUMAN
    AccessioniPrimary (citable) accession number: P49643
    Secondary accession number(s): Q53FJ8
    , Q6P1Q7, Q8WVL2, Q9H413
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: August 16, 2004
    Last modified: October 1, 2014
    This is version 125 of the entry and version 2 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

    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

    External Data

    Dasty 3