PDBsum entry 6ld3

Transferase

PDB id

6ld3

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Contents

			Protein chain

					578 a.a.

			Ligands

					G8O-FB2

			Metals

					_ZN ×2

			Waters ×215

PDB id:

6ld3

Links

Name:

Transferase

Title:

Zika ns5 polymerase domain

Structure:

RNA-directed RNA polymerase ns5. Chain: a. Synonym: ns5. Engineered: yes

Source:

Zika virus (isolate zikv/human/french polynesia/10087pf/2013). Zikv. Organism_taxid: 2043570. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

2.30Å

R-factor:

0.195

R-free:

0.249

Authors:

A.El Sahili,J.Lescar

Key ref:

A.Gharbi-Ayachi et al. Non-Nucleoside inhibitors of zika virus RNA-Dependent poly-Merase. To be published, . PubMed id: 32796069

Date:

20-Nov-19

Release date:

19-Aug-20

PROCHECK

	Headers

	References

Protein chain

A0A024B7W1 (POLG_ZIKVF) - Genome polyprotein from Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					3423 a.a. 578 a.a.

Key:

PfamA domain

Secondary structure



		Enzyme reactions

Enzyme class 1:

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 2:

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 3:

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 4:

E.C.3.4.21.91 - flavivirin.

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

Reaction:

Selective hydrolysis of Xaa-Xaa-|-Xbb bonds in which each of the Xaa can be either Arg or Lys and Xbb can be either Ser or Ala.

Enzyme class 5:

E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.

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

Reaction:

a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

ribonucleoside 5'-triphosphate	+	H2O	=	ribonucleoside 5'-diphosphate	+	phosphate	+	H(+)

Enzyme class 6:

E.C.3.6.4.13 - Rna helicase.

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

Reaction:

ATP + H2O = ADP + phosphate + H⁺

ATP	+	H2O	=	ADP	+	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