PDBsum entry 8e6c

Hydrolase, viral protein/inhibitor

PDB id

8e6c

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Contents

			Protein chain

					302 a.a.

			Ligands

					UTU

			Waters ×14

PDB id:

8e6c

Links

Name:

Hydrolase, viral protein/inhibitor

Title:

Crystal structure of mers 3cl protease in complex with a m- fluorophenyl dimethyl sulfane inhibitor

Structure:

Orf1a protein. Chain: a. Engineered: yes

Source:

Middle east respiratory syndrome-related coronavirus. Organism_taxid: 1335626. Gene: orf1a. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell: bl21(de3).

Resolution:

2.70Å

R-factor:

0.204

R-free:

0.259

Authors:

L.Liu,S.Lovell,K.P.Battaile,C.S.Dampalla,W.C.Groutas

Key ref:

S.Lovell and w.c.groutas Crystal structure of mers 3cl protease in complex wit m-Fluorophenyl dimethyl sulfane inhibitor. To be published, . PubMed id: 37080108

Date:

22-Aug-22

Release date:

07-Sep-22

PROCHECK

	Headers

	References

Protein chain

K9N7C7 (R1AB_CVEMC) - Replicase polyprotein 1ab from Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					7078 a.a. 302 a.a.*

Key:

PfamA domain

Secondary structure

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



		Enzyme reactions

Enzyme class 2:

E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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

Enzyme class 3:

E.C.2.1.1.57 - methyltransferase cap1.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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(+)

Enzyme class 4:

E.C.2.7.7.48 - RNA-directed Rna polymerase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n)	+	ribonucleoside 5'-triphosphate	=	RNA(n+1)	+	diphosphate

Enzyme class 5:

E.C.2.7.7.50 - mRNA guanylyltransferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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	+	H(+)	=	5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA	+	diphosphate

Enzyme class 6:

E.C.3.1.13.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Enzyme class 7:

E.C.3.4.19.12 - ubiquitinyl hydrolase 1.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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:

E.C.3.4.22.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Enzyme class 9:

E.C.3.6.4.12 - Dna helicase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

ATP + H2O = ADP + phosphate + H⁺

ATP	+	H2O	=	ADP	+	phosphate	+	H(+)

Enzyme class 10:

E.C.3.6.4.13 - Rna helicase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

ATP + H2O = ADP + phosphate + H⁺

ATP	+	H2O	=	ADP	+	phosphate	+	H(+)

Enzyme class 11:

E.C.4.6.1.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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