PDBsum entry: 1ymf

Hydrolase

PDB id: 1ymf

Contents

Protein chain

431 a.a. *

Ligands

ADP

Waters ×166

* Residue conservation analysis

PDB id:

1ymf

Name:

Hydrolase

Title:

Crystal structure of yellow fever virus ns3 helicase complexed with adp

Structure:

Genome polyprotein [contains: flavivirin protease ns3 catalytic subunit]. Chain: a. Fragment: sequence database residues 1671-2107 (portion of flavivirin protease ns3 catalytic subunit). Engineered: yes

Source:

Yellow fever virus. Organism_taxid: 11089. Strain: strain pasteur 17d-204. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.60Å R-factor: 0.199 R-free: 0.278

Authors:

J.Wu,A.K.Bera,R.J.Kuhn,J.L.Smith

Key ref:

J.Wu et al. (2005). Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing. J Virol, 79, 10268-10277. PubMed id: 16051820 DOI: 10.1128/JVI.79.16.10268-10277.2005

Date:

20-Jan-05 Release date: 23-Aug-05

Protein chain

P03314  (POLG_YEFV1) -  Genome polyprotein

Seq: 3411 a.a.

Struc: 431 a.a.*

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

Enzyme reactions

• Enzyme class 1: E.C.2.1.1.56 - mRNA (guanine-N(7)-)-methyltransferase.
• Reaction: S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m₇G(5')pppR-RNA

S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine (Bound ligand (Het Group name = ADP) matches with 51.00% similarity) + m(7)G(5')pppR-RNA

• Enzyme class 2: E.C.2.1.1.57 - mRNA (nucleoside-2'-O-)-methyltransferase.
• Reaction: S-adenosyl-L-methionine + m₇G(5')pppR-RNA = S-adenosyl-L-homocysteine + m₇G(5')pppRm-RNA

S-adenosyl-L-methionine + m(7)G(5')pppR-RNA = S-adenosyl-L-homocysteine (Bound ligand (Het Group name = ADP) matches with 51.00% similarity) + m(7)G(5')pppRm-RNA

• Enzyme class 3: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)

Nucleoside triphosphate (Bound ligand (Het Group name = ADP) matches with 53.00% similarity) + RNA(n) = diphosphate + RNA(n+1)

• Enzyme class 4: E.C.3.4.21.91 - Flavivirin.
• 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-triphosphatase.
• Reaction: NTP + H₂O = NDP + phosphate

NTP + H(2)O = NDP (Bound ligand (Het Group name = ADP) matches with 60.00% similarity) + phosphate

• Enzyme class 6: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H₂O = ADP + phosphate

ATP + H(2)O = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (3 terms)

reference

DOI no: 10.1128/JVI.79.16.10268-10277.2005

J Virol 79:10268-10277 (2005)

PubMed id: 16051820

Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing.

J.Wu, A.K.Bera, R.J.Kuhn, J.L.Smith.

ABSTRACT

Yellow fever virus (YFV), a member of the Flavivirus genus, has a plus-sense RNA genome encoding a single polyprotein. Viral protein NS3 includes a protease and a helicase that are essential to virus replication and to RNA capping. The 1.8-A crystal structure of the helicase region of the YFV NS3 protein includes residues 187 to 623. Two familiar helicase domains bind nucleotide in a triphosphate pocket without base recognition, providing a site for nonspecific hydrolysis of nucleoside triphosphates and RNA triphosphate. The third, C-terminal domain has a unique structure and is proposed to function in RNA and protein recognition. The organization of the three domains indicates that cleavage of the viral polyprotein NS3-NS4A junction occurs in trans.