PRI2_RAT
ID PRI2_RAT Reviewed; 507 AA.
AC O89044;
DT 29-AUG-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1998, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=DNA primase large subunit;
DE AltName: Full=DNA primase 58 kDa subunit;
DE Short=p58;
GN Name=Prim2;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=Sprague-Dawley; TISSUE=Liver;
RA Popanda O., Flohr C., Thielmann H.W.;
RT "A mutation in the gene of subunit II of DNA polymerase alpha from Novikoff
RT cells is concomitant with altered physico-chemical properties of the
RT enzyme.";
RL Submitted (SEP-1998) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Regulatory subunit of the DNA primase complex and component
CC of the DNA polymerase alpha complex (also known as the alpha DNA
CC polymerase-primase complex) which play an essential role in the
CC initiation of DNA synthesis (By similarity). During the S phase of the
CC cell cycle, the DNA polymerase alpha complex (composed of a catalytic
CC subunit POLA1, an accessory subunit POLA2 and two primase subunits, the
CC catalytic subunit PRIM1 and the regulatory subunit PRIM2) is recruited
CC to DNA at the replicative forks via direct interactions with MCM10 and
CC WDHD1 (By similarity). The primase subunit of the polymerase alpha
CC complex initiates DNA synthesis by oligomerising short RNA primers on
CC both leading and lagging strands (By similarity). These primers are
CC initially extended by the polymerase alpha catalytic subunit and
CC subsequently transferred to polymerase delta and polymerase epsilon for
CC processive synthesis on the lagging and leading strand, respectively.
CC In the primase complex, both subunits are necessary for the initial di-
CC nucleotide formation, but the extension of the primer depends only on
CC the catalytic subunit (By similarity). Binds RNA:DNA duplex and
CC coordinates the catalytic activities of PRIM1 and POLA2 during primase-
CC to-polymerase switch. {ECO:0000250|UniProtKB:P09884,
CC ECO:0000250|UniProtKB:P33610, ECO:0000250|UniProtKB:P49643}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000250|UniProtKB:P49643};
CC Note=Binds 1 [4Fe-4S] cluster. {ECO:0000250|UniProtKB:P49643};
CC -!- SUBUNIT: Heterodimer of a catalytic subunit PRIM1 and a regulatory
CC subunit PRIM2, also known as the DNA primase complex. Interacts via (C-
CC terminus) with PRIM1. Component of the alpha DNA polymerase complex
CC (also known as the alpha DNA polymerase-primase complex) consisting of
CC four subunits: the catalytic subunit POLA1, the regulatory subunit
CC POLA2, and the primase complex subunits PRIM1 and PRIM2 respectively
CC (By similarity). Within the complex, POLA1 directly interacts with
CC PRIM2 (By similarity). {ECO:0000250|UniProtKB:P33610,
CC ECO:0000250|UniProtKB:P49643}.
CC -!- DOMAIN: The RNA:DNA duplex-binding domain interacts with the template
CC phosphates at positions -2, -1, 1, and 2 positioning its bases -1, 1,
CC and 2 for duplex formation. Interacts only with the beta- and gamma-
CC phosphates of triphosphate moiety of initiating NTP of the primer. The
CC side chain of His-303 mimics a RNA base that would be paired with the
CC template nucleotide at position -1 via a hydrogen bond, thereby
CC facilitating the stacking of the initiating NTP. In the initiating
CC primosome a 'mini RNA:DNA' duplex is formed comprising three template
CC nucleotides at positions -1, 1, and 2 on one strand and His-303,
CC initiating NTP, and incoming NTP on the other strand.
CC {ECO:0000250|UniProtKB:P49643}.
CC -!- DOMAIN: The interdomain linker provides flexibility in movement
CC relative to primosome platform composed of PRIM1, the N-terminus of
CC PRIM2, the C-terminus of POLA1 and POLA2. Together with POLA1
CC interdomain linker, allows for large-scale conformational changes of
CC primosome and coordinated autoregulation of catalytic centers of PRIM1
CC and POLA1. It is proposed to move the C-terminus of PRIM2 close to
CC PRIM1 during initiation, then move it away with the 5'-end of the
CC nascent primer during elongation. The steric hindrance between the
CC N- and C-terminus of PRIM2 as the RNA primer is elongated limits its
CC length to 9 nucleotides. Ultimately a large rotation of the C-terminus
CC of PRIM2 transfers the primer to POLA1 active site for DNA synthesis.
CC {ECO:0000250|UniProtKB:P49643}.
CC -!- SIMILARITY: Belongs to the eukaryotic-type primase large subunit
CC family. {ECO:0000305}.
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DR EMBL; AJ011607; CAA09722.1; -; mRNA.
DR RefSeq; XP_006244748.1; XM_006244686.3.
DR RefSeq; XP_006244751.1; XM_006244689.3.
DR RefSeq; XP_006244752.1; XM_006244690.3.
DR RefSeq; XP_006244753.1; XM_006244691.2.
DR RefSeq; XP_017451824.1; XM_017596335.1.
DR RefSeq; XP_017451825.1; XM_017596336.1.
DR AlphaFoldDB; O89044; -.
DR SMR; O89044; -.
DR ComplexPortal; CPX-2089; DNA polymerase alpha:primase complex.
DR STRING; 10116.ENSRNOP00000016828; -.
DR jPOST; O89044; -.
DR PaxDb; O89044; -.
DR PRIDE; O89044; -.
DR Ensembl; ENSRNOT00000016828; ENSRNOP00000016828; ENSRNOG00000012486.
DR GeneID; 301323; -.
DR UCSC; RGD:631433; rat.
DR CTD; 5558; -.
DR RGD; 631433; Prim2.
DR eggNOG; KOG2267; Eukaryota.
DR GeneTree; ENSGT00390000009790; -.
DR HOGENOM; CLU_026253_2_0_1; -.
DR InParanoid; O89044; -.
DR OMA; KTSMPLC; -.
DR OrthoDB; 479347at2759; -.
DR PhylomeDB; O89044; -.
DR TreeFam; TF105893; -.
DR Reactome; R-RNO-113501; Inhibition of replication initiation of damaged DNA by RB1/E2F1.
DR Reactome; R-RNO-174411; Polymerase switching on the C-strand of the telomere.
DR Reactome; R-RNO-174430; Telomere C-strand synthesis initiation.
DR Reactome; R-RNO-68952; DNA replication initiation.
DR Reactome; R-RNO-68962; Activation of the pre-replicative complex.
DR Reactome; R-RNO-69091; Polymerase switching.
DR Reactome; R-RNO-69166; Removal of the Flap Intermediate.
DR Reactome; R-RNO-69183; Processive synthesis on the lagging strand.
DR PRO; PR:O89044; -.
DR Proteomes; UP000002494; Chromosome 9.
DR Bgee; ENSRNOG00000012486; Expressed in testis and 20 other tissues.
DR ExpressionAtlas; O89044; baseline and differential.
DR Genevisible; O89044; RN.
DR GO; GO:0005658; C:alpha DNA polymerase:primase complex; ISS:UniProtKB.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; ISS:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0071667; F:DNA/RNA hybrid binding; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; NAS:RGD.
DR GO; GO:0006270; P:DNA replication initiation; ISO:RGD.
DR GO; GO:0006269; P:DNA replication, synthesis of RNA primer; ISO:RGD.
DR GO; GO:1903934; P:positive regulation of DNA primase activity; ISS:UniProtKB.
DR CDD; cd07322; PriL_PriS_Eukaryotic; 1.
DR InterPro; IPR016558; DNA_primase_lsu_euk.
DR InterPro; IPR007238; DNA_primase_lsu_euk/arc.
DR PANTHER; PTHR10537; PTHR10537; 1.
DR Pfam; PF04104; DNA_primase_lrg; 1.
DR PIRSF; PIRSF009449; DNA_primase_large_subunit; 1.
PE 2: Evidence at transcript level;
KW 4Fe-4S; DNA replication; DNA-binding; Iron; Iron-sulfur; Metal-binding;
KW Phosphoprotein; Primosome; Reference proteome.
FT CHAIN 1..507
FT /note="DNA primase large subunit"
FT /id="PRO_0000046770"
FT REGION 253..270
FT /note="Interdomain linker"
FT /evidence="ECO:0000250|UniProtKB:P49643"
FT REGION 266..503
FT /note="Interacts with PRIM1"
FT /evidence="ECO:0000250|UniProtKB:P49643"
FT REGION 300..442
FT /note="RNA:DNA duplex binding"
FT /evidence="ECO:0000250|UniProtKB:P49643"
FT REGION 461..486
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 461..476
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 287
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P49643"
FT BINDING 367
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P49643"
FT BINDING 384
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P49643"
FT BINDING 424
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P49643"
FT MOD_RES 470
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P49643"
SQ SEQUENCE 507 AA; 58603 MW; 14859CA259DF054A CRC64;
MQFSGRTRKK LRLAGDQRNA CYPHSLQFYL QPPTENISLT EFESLAFDRV KLLKAIENLG
VSYVKGTEQY QSKLEAEIRK LKFSYRENLE DEYEPRRRDH ISHFILRLAY CQSEDLRRWF
IQQEMDLLRF RFSILPKDKV QSFLKDTHLH FEAISDEEKT LREQDIMASS PSLSGVRWES
ESVYKVPFAD ALDLFRGRKV YLEDGFAYVP LKDIVAIILN EFRATLSKAL ALTARSLPAV
QSDERLQPLL SHLSHSYTGQ DYSTQKSTGK ISLDQIDSLS TKSFPPCMRQ LHKALRENHH
LRHGGRMQYG LFLKGIGLTL EQALQFWKQE FIKGKMDPDK FDKGYSYNIR HSFGKEGKRT
DYTPFSCMKI ILTNPPSQGD FHGCPFRHSD AELLKQKMQT YKIPASGISQ ILDLVKGNHY
QVACQKYFEM THNVDDCGFS LNHPNQFFFE SQRILTGGKD IKKEASHPET PQHKPSTQKT
KDATSALASL DSSLEMDLEG LEDYFSK
