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Information on EC 2.7.7.102 - DNA primase AEP and Organism(s) Homo sapiens and UniProt Accession P49642

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EC Tree
     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.7 Nucleotidyltransferases
                2.7.7.102 DNA primase AEP
IUBMB Comments
The enzyme, which is found in eukaryota and archaea, catalyses the synthesis of short RNA or DNA sequences which are used as primers for EC 2.7.7.7, DNA-directed DNA polymerase.
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This record set is specific for:
Homo sapiens
UNIPROT: P49642
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The taxonomic range for the selected organisms is: Homo sapiens
The expected taxonomic range for this enzyme is: Eukaryota, Archaea
Reaction Schemes
hide
ssDNA
+
n
NTP
=
ssDNA/pppN(pN)n-1 hybrid
+
(n-1)
diphosphate
+
n
=
ssDNA/pppN(pN)n-1 hybrid
+
(n-1)
ssDNA
+
n
dNTP
=
ssDNA/pppdN(pdN)n-1 hybrid
+
(n-1)
diphosphate
+
n
=
ssDNA/pppdN(pdN)n-1 hybrid
+
(n-1)
Synonyms
protein orf904, ccdc111, prislx, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
AEP
-
-
-
-
archaeo-eukaryotic primase
-
-
-
-
DNA-directed primase/polymerase protein
-
PrimPol
SYSTEMATIC NAME
IUBMB Comments
(deoxy)nucleotide 5'-triphosphate:single-stranded DNA (deoxy)nucleotidyltransferase (DNA or DNA-RNA hybrid synthesizing)
The enzyme, which is found in eukaryota and archaea, catalyses the synthesis of short RNA or DNA sequences which are used as primers for EC 2.7.7.7, DNA-directed DNA polymerase.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
M13 ssDNA + n dNTP
M13 ssDNA/pppdN(pdN)n-1 + (n-1) diphosphate
show the reaction diagram
-
-
-
?
M13 ssDNA + n NTP
M13 ssDNA/pppN(pN)n-1 + (n-1) diphosphate
show the reaction diagram
-
-
-
?
additional information
?
-
a template oligonucleotide in which sequence GTCC is flanked by thymine residues is also recognized as substrate, with preferential formation of initiating dinucleotides 5'-A-dG-3' or 5'-dA-dG-3'
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
[4Fe-4S]-center
cluster is buried deeply within the protein core
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
presence of Mn2+ is required
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
KCl
in the presence of Mg2+, primase activity is inhibited almost 4fold by increasing the KCl concentration from 15 mM to 150 mM. In the presence of Mn2+, KCl stimulates RNA synthesis
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Mn2+
significantly enhances the binding of nucleotide to primase,which correlates with higher catalytic efficiency in vitro
KCl
in the presence of Mg2+, primase activity is inhibited almost 4fold by increasing the KCl concentration from 15 mM to 150 mM. In the presence of Mn2+, KCl stimulates RNA synthesis
additional information
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
subunit Prim1
UniProt
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
PRI1_HUMAN
420
0
49902
Swiss-Prot
other Location (Reliability: 1)
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
structure of the catalytic subunit, with bound UTP and Mn2+. Primase contains the conserved catalytic prim fold domain, with a subdomain different from the archaeal and bacterial primases. Residues S160 and H166 are in direct contact with UTP
strcuture of the highly conserved C-terminal regulatory domain of the large subunit to 1.7 A resolution. The evolutionarily conserved 4Fe-4S cluster is buried deeply within the protein core. DNA binding shows a strong preference for ss/dsDNA junction substrates. The enzyme interacts specifically with the C-terminal domain of the intermediate subunit of replication protein A, RPA32C
structure of small subunit Prim1 at 2.2 A resolution, with citrate in its inactive forms. Dibasic citrate is bound at the nucleotide triphosphate beta, gamma-phosphate binding site through nine hydrogen bonds. The activity of Prim1 is regulated by pH and citrate
structure of the complex Prim1/Prim2, at 2.65 A resolution, and modeling of the protein in complex with NTP and DNA/RNA substrates
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D114A/E116A
mutant in two potential metal bindig sites, inactive
H299D
10fold reduction in affinity for replication protein A
R302
50fold reduction in affinity for replication protein A
additional information
construction of deletion mutants lacking residues of the linker between the C-terminal and N-terminal regions of subunit Prim2 or having an insertion. Deletion of 15 amino acids of the linker decreases activity about 5fold. The enzyme with a longer linker has the same activity as wild type. Deletion of the C-terminus results in complete loss of the ability to initiate primer synthesis
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lee, J.; Park, K.; An, J.; Kang, J.; Shen, H.; Wang, J.; Eom, S.
Structural and biochemical insights into inhibition of human primase by citrate
Biochem. Biophys. Res. Commun.
507
383-388
2018
Homo sapiens (P49642 and P09884)
Manually annotated by BRENDA team
Baranovskiy, A.; Zhang, Y.; Suwa, Y.; Babayeva, N.; Gu, J.; Pavlov, Y.; Tahirov, T.
Crystal structure of the human primase
J. Biol. Chem.
290
5635-5646
2015
Homo sapiens (P49642 and P49643)
Manually annotated by BRENDA team
Baranovskiy, A.; Zhang, Y.; Suwa, Y.; Gu, J.; Babayeva, N.; Pavlov, Y.; Tahirov, T.
Insight into the human DNA primase interaction with template-primer
J. Biol. Chem.
291
4793-4802
2016
Homo sapiens (P49642 and P49643)
Manually annotated by BRENDA team
Vaithiyalingam, S.; Arnett, D.R.; Aggarwal, A.; Eichman, B.F.; Fanning, E.; Chazin, W.J.
Insights into eukaryotic primer synthesis from structures of the p48 subunit of human DNA primase
J. Mol. Biol.
426
558-569
2014
Homo sapiens (P49642), Homo sapiens (P49642 and P49643), Saccharomyces cerevisiae (P10363)
Manually annotated by BRENDA team
Garcia-Gomez, S.; Reyes, A.; Martinez-Jimenez, M.I.; Chocron, E.S.; Mouron, S.; Terrados, G.; Powell, C.; Salido, E.; Mendez, J.; Holt, I.J.; Blanco, L.
PrimPol, an archaic primase/polymerase operating in human cells
Mol. Cell
52
541-553
2013
Homo sapiens (Q96LW4)
Manually annotated by BRENDA team
Bergsch, J.; Allain, F.H.; Lipps, G.
Recent advances in understanding bacterial and archaeoeukaryotic primases
Curr. Opin. Struct. Biol.
59
159-167
2019
Homo sapiens (Q96LW4)
Manually annotated by BRENDA team