PDBsum entry 3r24

Transferase, viral protein

PDB id: 3r24

Contents

Protein chains

292 a.a.

121 a.a.

Ligands

SAM

Metals

_ZN ×2

Waters ×467

PDB id:

3r24

Name:

Transferase, viral protein

Title:

Crystal structure of nsp10/nsp16 complex of sars coronavirus

Structure:

2'-o-methyl transferase. Chain: a. Synonym: nsp16. Engineered: yes. Non-structural protein 10 and non-structural protein 11. Chain: b. Fragment: unp residues 4240-4382. Synonym: nsp10, growth factor-like peptide, gfl, nsp11. Engineered: yes

Source:

Sars coronavirus. Sars-cov. Organism_taxid: 227859. Gene: rep, 1a-1b. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: 1a.

Resolution:

2.00Å R-factor: 0.195 R-free: 0.222

Authors:

X.Liu,D.Guo,C.Su,Y.Chen

Key ref:

Y.Chen et al. (2011). Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex. Plos Pathog, 7, e1002294. PubMed id: 22022266

Date:

13-Mar-11 Release date: 26-Oct-11

Protein chain

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

Seq: 7073 a.a.

Struc: 292 a.a.

Protein chain

P0C6U8  (R1A_CVHSA) -  Replicase polyprotein 1a from Severe acute respiratory syndrome coronavirus

Seq: 4382 a.a.

Struc: 121 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: Chain A: E.C.2.1.1.- - ?????
• Enzyme class 2: Chain A: 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 (Bound ligand (Het Group name = SAM) corresponds exactly) = 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine

• Enzyme class 3: 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 4: Chain A: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 5: Chains A, B: 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 = SAM) matches with 43.90% similarity) + H(+) = 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate

• Enzyme class 6: Chain A: E.C.3.1.13.- - ?????
• Enzyme class 7: 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 8: Chains A, B: E.C.3.4.22.- - ?????
• Enzyme class 9: Chains A, B: E.C.3.4.22.69 - Sars coronavirus main proteinase.
• Enzyme class 10: 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 11: 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(+)

• Enzyme class 12: Chain A: 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

Plos Pathog 7:e1002294 (2011)

PubMed id: 22022266

Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex.

Y.Chen, C.Su, M.Ke, X.Jin, L.Xu, Z.Zhang, A.Wu, Y.Sun, Z.Yang, P.Tien, T.Ahola, Y.Liang, X.Liu, D.Guo.

ABSTRACT

No abstract given.