Function and Biology

CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1

Source organisms:
Biochemical function: DNA binding
Biological process: DNA replication
Cellular component: primosome complex

EC 2.7.7.102: DNA primase AEP

Reaction catalysed:
SsDNA + n NTP = ssDNA/pppN(pN)(n-1) hybrid + (n-1) diphosphate
Systematic name:
(Deoxy)nucleotide 5'-triphosphate:single-stranded DNA (deoxy)nucleotidyltransferase (DNA or DNA-RNA hybrid synthesizing)
Alternative Name(s):
  • AEP
  • Archaeo-eukaryotic primase
  • PrimPol

EC 3.4.22.69: SARS coronavirus main proteinase

Reaction catalysed:
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
Systematic name:
-
Alternative Name(s):
  • 3C-like protease
  • 3cLpro
  • Coronavirus 3C-like protease
  • Mpro
  • SARS 3C-like protease
  • SARS coronavirus 3CL protease
  • SARS coronavirus main peptidase
  • SARS coronavirus main protease
  • SARS-CoV 3CLpro enzyme
  • SARS-CoV Mpro
  • SARS-CoV main protease
  • Severe acute respiratory syndrome coronavirus main protease

EC 3.4.19.12: Ubiquitinyl hydrolase 1

Reaction catalysed:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Systematic name:
-
Alternative Name(s):
  • Ubiquitin C-terminal hydrolase
  • Ubiquitin carboxyl-terminal hydrolase
  • Ubiquitin thiolesterase
  • Yeast ubiquitin hydrolase

EC 2.7.7.50: mRNA guanylyltransferase

Reaction catalysed:
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
Systematic name:
GTP:mRNA guanylyltransferase
Alternative Name(s):
  • GTP--RNA guanylyltransferase
  • Messenger RNA guanylyltransferase
  • Protein lambda-2
  • mRNA capping enzyme

EC 2.7.7.7: DNA-directed DNA polymerase

Reaction catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Systematic name:
Deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed)
Alternative Name(s):
  • DNA duplicase
  • DNA nucleotidyltransferase
  • DNA nucleotidyltransferase (DNA-directed)
  • DNA polymerase
  • DNA polymerase I
  • DNA polymerase II
  • DNA polymerase III
  • DNA polymerase alpha
  • DNA polymerase beta
  • DNA polymerase gamma
  • DNA replicase
  • DNA-dependent DNA polymerase
  • Deoxynucleate polymerase
  • Deoxyribonucleate nucleotidyltransferase
  • Deoxyribonucleic acid duplicase
  • Deoxyribonucleic acid polymerase
  • Deoxyribonucleic duplicase
  • Deoxyribonucleic polymerase
  • Deoxyribonucleic polymerase I
  • Duplicase
  • Klenow fragment
  • Sequenase
  • Taq DNA polymerase
  • Taq Pol I
  • Tca DNA polymerase

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF11501
Domain description: Betacoronavirus replicase NSP1
Occurring in:
  1. Host translation inhibitor nsp1
The deposited structure of PDB entry 7opl contains 1 copy of Pfam domain PF11501 (Betacoronavirus replicase NSP1) in Host translation inhibitor nsp1. Showing 1 copy in chain E.

PF04104
Domain description: Eukaryotic and archaeal DNA primase, large subunit
Occurring in:
  1. DNA primase large subunit
The deposited structure of PDB entry 7opl contains 1 copy of Pfam domain PF04104 (Eukaryotic and archaeal DNA primase, large subunit) in DNA primase large subunit. Showing 1 copy in chain D.

PF01896
Domain description: DNA primase small subunit
Occurring in:
  1. DNA primase small subunit
The deposited structure of PDB entry 7opl contains 1 copy of Pfam domain PF01896 (DNA primase small subunit) in DNA primase small subunit. Showing 1 copy in chain C.

PF04042
Domain description: DNA polymerase alpha/epsilon subunit B
Occurring in:
  1. DNA polymerase alpha subunit B
The deposited structure of PDB entry 7opl contains 1 copy of Pfam domain PF04042 (DNA polymerase alpha/epsilon subunit B) in DNA polymerase alpha subunit B. Showing 1 copy in chain B.

PF22062
Domain description: DNA polymerase alpha subunit B, OB domain
Occurring in:
  1. DNA polymerase alpha subunit B
The deposited structure of PDB entry 7opl contains 1 copy of Pfam domain PF22062 (DNA polymerase alpha subunit B, OB domain) in DNA polymerase alpha subunit B. Showing 1 copy in chain B.

PF08996
Domain description: DNA Polymerase alpha zinc finger
Occurring in:
  1. DNA polymerase alpha catalytic subunit
The deposited structure of PDB entry 7opl contains 1 copy of Pfam domain PF08996 (DNA Polymerase alpha zinc finger) in DNA polymerase alpha catalytic subunit. Showing 1 copy in chain A.

PF00136
Domain description: DNA polymerase family B
Occurring in:
  1. DNA polymerase alpha catalytic subunit
The deposited structure of PDB entry 7opl contains 1 copy of Pfam domain PF00136 (DNA polymerase family B) in DNA polymerase alpha catalytic subunit. Showing 1 copy in chain A.

PF03104
Domain description: DNA polymerase family B, exonuclease domain
Occurring in:
  1. DNA polymerase alpha catalytic subunit
The deposited structure of PDB entry 7opl contains 1 copy of Pfam domain PF03104 (DNA polymerase family B, exonuclease domain) in DNA polymerase alpha catalytic subunit. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR006172
Domain description: DNA-directed DNA polymerase, family B
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR007238
Domain description: DNA primase large subunit, eukaryotic/archaeal
Occurring in:
  1. DNA primase large subunit
IPR016558
Domain description: DNA primase, large subunit, eukaryotic
Occurring in:
  1. DNA primase large subunit
IPR014052
Domain description: DNA primase, small subunit, eukaryotic/archaeal
Occurring in:
  1. DNA primase small subunit
IPR016722
Domain description: DNA polymerase alpha, subunit B
Occurring in:
  1. DNA polymerase alpha subunit B
IPR038030
Domain description: NSP1 globular domain superfamily, betacoronavirus
Occurring in:
  1. Host translation inhibitor nsp1
IPR021590
Domain description: NSP1, globular domain, betacoronavirus
Occurring in:
  1. Host translation inhibitor nsp1
IPR046443
Domain description: NSP1, globular domain, alpha/betacoronavirus
Occurring in:
  1. Host translation inhibitor nsp1
IPR002755
Domain description: DNA primase, small subunit
Occurring in:
  1. DNA primase small subunit
IPR007185
Domain description: DNA polymerase alpha/delta/epsilon, subunit B
Occurring in:
  1. DNA polymerase alpha subunit B
IPR013627
Domain description: DNA polymerase alpha, subunit B, N-terminal
Occurring in:
  1. DNA polymerase alpha subunit B
IPR015088
Domain description: Zinc finger, DNA-directed DNA polymerase, family B, alpha
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR038256
Domain description: DNA polymerase alpha, zinc finger domain superfamily
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR042087
Domain description: DNA polymerase family B, thumb domain
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR017964
Domain description: DNA-directed DNA polymerase, family B, conserved site
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR045846
Domain description: DNA polymerase alpha catalytic subunit, catalytic domain
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR023211
Domain description: DNA polymerase, palm domain superfamily
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR043502
Domain description: DNA/RNA polymerase superfamily
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR006134
Domain description: DNA-directed DNA polymerase, family B, multifunctional domain
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR036397
Domain description: Ribonuclease H superfamily
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR012337
Domain description: Ribonuclease H-like superfamily
Occurring in:
  1. DNA polymerase alpha catalytic subunit
IPR006133
Domain description: DNA-directed DNA polymerase, family B, exonuclease domain
Occurring in:
  1. DNA polymerase alpha catalytic subunit