PDBsum entry 5yn6

Transferase

PDB id: 5yn6

Contents

Protein chains

283 a.a.

120 a.a.

Ligands

SAM

Metals

_ZN ×2

Waters ×128

PDB id:

5yn6

Name:

Transferase

Title:

Crystal structure of mers-cov nsp10/nsp16 complex bound to sam

Structure:

Nsp16 protein. Chain: a. Engineered: yes. Nsp10 protein. Chain: b. Engineered: yes

Source:

Human betacoronavirus 2c emc/2012. Organism_taxid: 1235996. Gene: orf1ab. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.95Å R-factor: 0.196 R-free: 0.227

Authors:

S.M.Wei,L.Yang,Z.H.Ke,D.Y.Guo,C.P.Fan

Key ref:

S.M.Wei et al. Structural insights into the molecular mechanism of m coronavirus RNA ribose 2'-O-Methylation by nsp16/nsp1 protein complex. To be published, .

Date:

24-Oct-17 Release date: 05-Dec-18

Protein chain

K0BWD0  (K0BWD0_MERS) -  ORF1ab polyprotein from Human betacoronavirus 2c EMC/2012

Seq: 7078 a.a.

Struc: 283 a.a.

Protein chain

K4LC41  (K4LC41_MERS) -  ORF1a from Human betacoronavirus 2c EMC/2012

Seq: 4391 a.a.

Struc: 120 a.a.

Enzyme reactions

• Enzyme class 1: Chain A: 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 (Bound ligand (Het Group name = SAM) corresponds exactly) = 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H(+)

• Enzyme class 2: Chains A, B: 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 3: Chain A: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = SAM) matches with 50.00% similarity) + phosphate + H(+)

• Enzyme class 4: Chain A: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = SAM) matches with 50.00% similarity) + phosphate + H(+)

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