PDBsum entry 3gpq

Viral protein/RNA

PDB id: 3gpq

Contents

Protein chains

160 a.a. *

150 a.a. *

148 a.a. *

Ligands

_DA-_DA ×2

Waters ×250

* Residue conservation analysis

PDB id:

3gpq

Name:

Viral protein/RNA

Title:

Crystal structure of macro domain of chikungunya virus in complex with RNA

Structure:

Non-structural protein 3. Chain: a, b, c, d. Fragment: sequence database residues 1334-1493. Synonym: nsp3. Engineered: yes. RNA (5'-r( Ap Ap A)-3'). Chain: e, f. Engineered: yes

Source:

Chikungunya virus. Organism_taxid: 371094. Strain: ross. Gene: nsp3. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Resolution:

2.00Å R-factor: 0.218 R-free: 0.260

Authors:

H.Malet,S.Jamal,B.Coutard,B.Canard

Key ref:

H.Malet et al. (2009). The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket. J Virol, 83, 6534-6545. PubMed id: 19386706

Date:

23-Mar-09 Release date: 21-Jul-09

Protein chains

Q8JUX6  (POLN_CHIKS) -  Polyprotein P1234 from Chikungunya virus (strain S27-African prototype)

Seq: 2474 a.a.

Struc: 160 a.a.

Protein chain

Q8JUX6  (POLN_CHIKS) -  Polyprotein P1234 from Chikungunya virus (strain S27-African prototype)

Seq: 2474 a.a.

Struc: 150 a.a.*

Protein chain

Q8JUX6  (POLN_CHIKS) -  Polyprotein P1234 from Chikungunya virus (strain S27-African prototype)

Seq: 2474 a.a.

Struc: 148 a.a.

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

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D: E.C.2.1.1.- - ?????
• Enzyme class 2: Chains A, B, C, D: E.C.2.7.7.- - ?????
• Enzyme class 3: Chains A, B, C, D: E.C.2.7.7.19 - polynucleotide adenylyltransferase.
• Reaction: RNA(n) + ATP = RNA(n)-3'-adenine ribonucleotide + diphosphate
• Enzyme class 4: Chains A, B, C, D: 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, C, D: E.C.3.1.3.84 - ADP-ribose 1''-phosphate phosphatase.
• Reaction: ADP-alpha-D-ribose 1''-phosphate + H2O = ADP-D-ribose + phosphate
• Enzyme class 6: Chains A, B, C, D: E.C.3.4.22.- - ?????
• Enzyme class 7: Chains A, B, C, D: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 8: Chains A, B, C, D: E.C.3.6.1.74 - mRNA 5'-phosphatase.
• Reaction: a 5'-end triphospho-ribonucleoside in mRNA + H2O = a 5'-end diphospho- ribonucleoside in mRNA + phosphate + H⁺
• Enzyme class 9: Chains A, B, C, D: 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

J Virol 83:6534-6545 (2009)

PubMed id: 19386706

The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket.

H.Malet, B.Coutard, S.Jamal, H.Dutartre, N.Papageorgiou, M.Neuvonen, T.Ahola, N.Forrester, E.A.Gould, D.Lafitte, F.Ferron, J.Lescar, A.E.Gorbalenya, X.de Lamballerie, B.Canard.

ABSTRACT

Macro domains (also called "X domains") constitute a protein module family present in all kingdoms of life, including viruses of the Coronaviridae and Togaviridae families. Crystal structures of the macro domain from the Chikungunya virus (an "Old World" alphavirus) and the Venezuelan equine encephalitis virus (a "New World" alphavirus) were determined at resolutions of 1.65 and 2.30 A, respectively. These domains are active as adenosine di-phosphoribose 1''-phosphate phosphatases. Both the Chikungunya and the Venezuelan equine encephalitis virus macro domains are ADP-ribose binding modules, as revealed by structural and functional analysis. A single aspartic acid conserved through all macro domains is responsible for the specific binding of the adenine base. Sequence-unspecific binding to long, negatively charged polymers such as poly(ADP-ribose), DNA, and RNA is observed and attributed to positively charged patches outside of the active site pocket, as judged by mutagenesis and binding studies. The crystal structure of the Chikungunya virus macro domain with an RNA trimer shows a binding mode utilizing the same adenine-binding pocket as ADP-ribose, but avoiding the ADP-ribose 1''-phosphate phosphatase active site. This leaves the AMP binding site as the sole common feature in all macro domains.