PDBsum entry 3vtt

Viral protein, structural protein

PDB id: 3vtt

Contents

Protein chains

100 a.a.

Ligands

SO4 ×2

Waters ×146

PDB id:

3vtt

Name:

Viral protein, structural protein

Title:

High resolution crystal structure of dengue 3 envelope protein domain iii (ed3)

Structure:

Envelope protein e. Chain: a, b. Fragment: unp residues 574-678. Engineered: yes

Source:

Dengue virus type 3. Denv-3. Organism_taxid: 408870. Strain: philippines/h87/1956. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.208 R-free: 0.255

Authors:

M.Elahi,M.M.Islam,Y.Kuroda

Key ref:

M.Elahi et al. (2013). High resolution crystal structure of dengue-3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition. Proteins, 81, 1090-1095. PubMed id: 23239402 DOI: 10.1002/prot.24237

Date:

07-Jun-12 Release date: 26-Dec-12

Protein chains

P27915  (POLG_DEN3P) -  Genome polyprotein from Dengue virus type 3 (strain Philippines/H87/1956)

Seq: 3390 a.a.

Struc: 100 a.a.

Enzyme reactions

• Enzyme class 1: 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
• Enzyme class 2: 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⁺
• Enzyme class 3: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• 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-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 6: E.C.3.6.4.13 - Rna helicase.
• Reaction: 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

reference

DOI no: 10.1002/prot.24237

Proteins 81:1090-1095 (2013)

PubMed id: 23239402

High resolution crystal structure of dengue-3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition.

M.Elahi, M.M.Islam, K.Noguchi, M.Yohda, Y.Kuroda.

ABSTRACT

Dengue viruses are classified into four serotypes. Here, we report a 1.7 Å crystal structure of a recombinant dengue-3 envelope protein domain III (ED3), which contains most of the putative epitopes. Although the fold was well conserved, we found that a local backbone deformation in the first β-strand, which contains the putative epitope-1, occurred upon domain isolation. Furthermore, a comparison with dengue-2 ED3 indicated a large structural change by as much as 4.0 Å at Asp(662) , located in epitope-2. These minute structural and surface properties changes observed in the high resolution ED3 structure represent potential determinants for serospecificity and epitope recognition by antibodies. © 2012 Wiley Periodicals, Inc.