PDBsum entry 5c8s

Transferase

PDB id: 5c8s

Contents

Protein chains

133 a.a.

514 a.a.

Ligands

SAH ×2

G3A ×2

Metals

_ZN ×10

_MG ×2

PDB id:

5c8s

Name:

Transferase

Title:

Crystal structure of the sars coronavirus nsp14-nsp10 complex with functional ligands sah and gpppa

Structure:

Non-structural protein 10. Chain: a, c. Synonym: nsp10. Engineered: yes. Guanine-n7 methyltransferase. Chain: b, d. Synonym: nsp14. Engineered: yes

Source:

Human sars coronavirus. Sars-cov. Organism_taxid: 227859. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.33Å R-factor: 0.219 R-free: 0.259

Authors:

Y.Y.Ma,L.J.Wu,R.G.Zhang,Z.H.Rao

Key ref:

Y.Ma et al. (2015). Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex. Proc Natl Acad Sci U S A, 112, 9436-9441. PubMed id: 26159422 DOI: 10.1073/pnas.1508686112

Date:

26-Jun-15 Release date: 15-Jul-15

Protein chains

P0C6X7  (R1AB_CVHSA) -  Replicase polyprotein 1ab from Severe acute respiratory syndrome coronavirus

Seq: 7073 a.a.

Struc: 133 a.a.*

Protein chains

P0C6X7  (R1AB_CVHSA) -  Replicase polyprotein 1ab from Severe acute respiratory syndrome coronavirus

Seq: 7073 a.a.

Struc: 514 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D: E.C.2.1.1.- - ?????
• Enzyme class 3: Chains A, B, C, D: E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.
• Reaction: a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine

5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine (Bound ligand (Het Group name = SAH) corresponds exactly)

• Enzyme class 4: Chains A, B, C, D: E.C.2.1.1.57 - methyltransferase cap1.
• Reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺

5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

• Enzyme class 5: Chains A, B, C, D: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 6: Chains A, B, C, D: E.C.2.7.7.50 - mRNA guanylyltransferase.
• Reaction: a 5'-end diphospho-ribonucleoside in mRNA + GTP + H⁺ = a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate

5'-end diphospho-ribonucleoside in mRNA + GTP (Bound ligand (Het Group name = G3A) matches with 64.00% similarity) + H(+) = 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate

• Enzyme class 7: Chains A, B, C, D: E.C.3.1.13.- - ?????
• Enzyme class 8: Chains A, B, C, D: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, 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).
• Enzyme class 9: Chains A, B, C, D: E.C.3.4.22.- - ?????
• Enzyme class 10: Chains A, B, C, D: E.C.3.4.22.69 - Sars coronavirus main proteinase.
• Enzyme class 11: Chains A, B, C, D: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP (Bound ligand (Het Group name = G3A) matches with 62.00% similarity) + H2O = ADP + phosphate + H(+)

• Enzyme class 12: Chains A, B, C, D: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP (Bound ligand (Het Group name = G3A) matches with 62.00% similarity) + H2O = ADP + phosphate + H(+)

• Enzyme class 13: Chains A, B, C, D: E.C.4.6.1.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1508686112

Proc Natl Acad Sci U S A 112:9436-9441 (2015)

PubMed id: 26159422

Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex.

Y.Ma, L.Wu, N.Shaw, Y.Gao, J.Wang, Y.Sun, Z.Lou, L.Yan, R.Zhang, Z.Rao.

ABSTRACT

Nonstructural protein 14 (nsp14) of coronaviruses (CoV) is important for viral replication and transcription. The N-terminal exoribonuclease (ExoN) domain plays a proofreading role for prevention of lethal mutagenesis, and the C-terminal domain functions as a (guanine-N7) methyl transferase (N7-MTase) for mRNA capping. The molecular basis of both these functions is unknown. Here, we describe crystal structures of severe acute respiratory syndrome (SARS)-CoV nsp14 in complex with its activator nonstructural protein10 (nsp10) and functional ligands. One molecule of nsp10 interacts with ExoN of nsp14 to stabilize it and stimulate its activity. Although the catalytic core of nsp14 ExoN is reminiscent of proofreading exonucleases, the presence of two zinc fingers sets it apart from homologs. Mutagenesis studies indicate that both these zinc fingers are essential for the function of nsp14. We show that a DEEDh (the five catalytic amino acids) motif drives nucleotide excision. The N7-MTase domain exhibits a noncanonical MTase fold with a rare β-sheet insertion and a peripheral zinc finger. The cap-precursor guanosine-P3-adenosine-5',5'-triphosphate and S-adenosyl methionine bind in proximity in a highly constricted pocket between two β-sheets to accomplish methyl transfer. Our studies provide the first glimpses, to our knowledge, into the architecture of the nsp14-nsp10 complex involved in RNA viral proofreading.