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Crystal structure of N-terminal SARS-CoV-2 nsp1 in complex with fragment hit 9D4 refined against the anomalous diffraction data

Source organism: Severe acute respiratory syndrome coronavirus 2
Biochemical function: not assigned
Biological process: not assigned
Cellular component: not assigned

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EC 3.6.4.13: RNA helicase

Reaction catalysed:
ATP + H(2)O = ADP + phosphate
Systematic name:
ATP phosphohydrolase (RNA helix unwinding)
Alternative Name(s):
  • CSFV NS3 helicase
  • DBP2
  • DDX17
  • DDX25
  • DDX3
  • DDX3X
  • DDX3Y
  • DDX4
  • DDX5
  • DEAD-box RNA helicase
  • DEAD-box protein DED1
  • DEAH-box RNA helicase
  • DEAH-box protein 2
  • DED1
  • DbpA
  • Dex(H/D) RNA helicase
  • EIF4A helicase
  • EhDEAD1
  • EhDEAD1 RNA helicase
  • GRTH/DDX25
  • KOKV helicase
  • Mtr4p
  • NPH-II
  • Nonstructural protein 3 helicase
  • RHA
  • RNA helicase A
  • RNA helicase DDX3
  • RNA helicase Hera
  • RNA-dependent ATPase
  • TGBp1 NTPase/helicase domain
  • VRH1

EC 3.6.4.12: DNA helicase

Reaction catalysed:
ATP + H(2)O = ADP + phosphate
Systematic name:
ATP phosphohydrolase (DNA helix unwinding)
Alternative Name(s):
  • 3' to 5' DNA helicase
  • 3'-5' DNA helicase
  • 3'-5' PfDH
  • 5' to 3' DNA helicase
  • AvDH1
  • BACH1 helicase
  • BLM protein
  • BRCA1-associated C-terminal helicase
  • BcMCM
  • CeWRN-1
  • DNA helicase 120
  • DNA helicase A
  • DNA helicase E
  • DNA helicase II
  • DNA helicase III
  • DNA helicase RECQL5'
  • DNA helicase VI
  • Dbp9p
  • DmRECQ5
  • DnaB
  • DnaB helicase E1
  • HHcsA
  • HPif1
  • Hel E
  • Helicase DnaB
  • Helicase HDH IV
  • Helicase domain of bacteriophage T7 gene 4 protein helicase
  • Hmi1p
  • MCM helicase
  • MCM protein
  • MER3 helicase
  • MER3 protein
  • MPH1
  • PDH120
  • PIF1
  • PcrA
  • PcrA helicase
  • PfDH A
  • Pfh1p
  • UvrD

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 2.7.7.48: RNA-directed RNA polymerase

Reaction catalysed:
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Systematic name:
Nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)
Alternative Name(s):
  • 3D polymerase
  • PB1 proteins
  • PB2 proteins
  • Phage f2 replicase
  • Polymerase L
  • Q-beta replicase
  • RDRP
  • RNA nucleotidyltransferase (RNA-directed)
  • RNA replicase
  • RNA synthetase
  • RNA transcriptase
  • RNA-dependent RNA polymerase
  • RNA-dependent RNA replicase
  • RNA-dependent ribonucleate nucleotidyltransferase
  • Ribonucleic acid replicase
  • Ribonucleic acid-dependent ribonucleate nucleotidyltransferase
  • Ribonucleic acid-dependent ribonucleic acid polymerase
  • Ribonucleic replicase
  • Ribonucleic synthetase
  • Transcriptase

EC 2.1.1.57: Methyltransferase cap1

Reaction catalysed:
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Systematic name:
S-adenosyl-L-methionine:5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] 2-O-methyltransferase
Alternative Name(s):
  • Cap1-MTase
  • MTR1
  • Messenger RNA (nucleoside-2'-)-methyltransferase
  • Messenger ribonucleate nucleoside 2'-methyltransferase
  • S-adenosyl-L-methionine:mRNA (nucleoside-2'-O)-methyltransferase
  • mRNA (nucleoside-2'-O)-methyltransferase

EC 2.1.1.56: mRNA (guanine-N(7))-methyltransferase

Reaction catalysed:
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
Systematic name:
S-adenosyl-L-methionine:mRNA (guanine-N(7))-methyltransferase
Alternative Name(s):
  • Guanine-7-methyltransferase
  • Messenger RNA guanine 7-methyltransferase
  • Messenger ribonucleate guanine 7-methyltransferase
  • S-adenosyl-L-methionine:mRNA (guanine-7-N)-methyltransferase

GO terms

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Sequence family

Pfam Protein family (Pfam)
PF11501
Domain description: Betacoronavirus replicase NSP1
Occurring in:
  1. Host translation inhibitor nsp1
The deposited structure of PDB entry 8rf4 contains 1 copy of Pfam domain PF11501 (Betacoronavirus replicase NSP1) in Host translation inhibitor nsp1. Showing 1 copy in chain A.

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