PDBsum entry 4ckc

Transferase/hydrolase

PDB id: 4ckc

Contents

Protein chains

819 a.a.

284 a.a.

Ligands

SAH ×2

Waters ×82

PDB id:

4ckc

Name:

Transferase/hydrolase

Title:

Vaccinia virus capping enzyme complexed with sah (monoclinic form)

Structure:

mRNA-capping enzyme catalytic subunit. Chain: a, d. Synonym: virus termination factor large subunit, vtf large subunit, mRNA-capping enzyme 97 kda subunit, mRNA-capping enzyme d1 subunit, mRNA-capping enzyme large subunit, polynucleotide 5'-triphosphatase, mRNA 5'-triphosphatase, tpase, mRNA guanylyltransferase, gtp--RNA guanylyltransferase, gtase, mRNA (guanine-n(7)-)-methyltransferase, mRNA cap methyltransferase. Engineered: yes.

Source:

Vaccinia virus. Organism_taxid: 10245. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: star plyss.

Resolution:

2.90Å R-factor: 0.257 R-free: 0.297

Authors:

O.J.P.Kyrieleis,J.Chang,M.De La Pena,S.Shuman,S.Cusack

Key ref:

O.J.Kyrieleis et al. (2014). Crystal structure of vaccinia virus mRNA capping enzyme provides insights into the mechanism and evolution of the capping apparatus. Structure, 22, 452-465. PubMed id: 24607143 DOI: 10.1016/j.str.2013.12.014

Date:

02-Jan-14 Release date: 19-Mar-14

Protein chains

P04298  (MCEL_VACCW) -  mRNA-capping enzyme catalytic subunit from Vaccinia virus (strain Western Reserve)

Seq: 844 a.a.

Struc: 819 a.a.

Protein chains

P04318  (MCES_VACCW) -  mRNA-capping enzyme regulatory subunit OPG124 from Vaccinia virus (strain Western Reserve)

Seq: 287 a.a.

Struc: 284 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, D: 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

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 (Bound ligand (Het Group name = SAH) corresponds exactly)

• Enzyme class 2: Chains A, D: E.C.2.7.7.50 - mRNA guanylyltransferase.
• 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 (Bound ligand (Het Group name = SAH) matches with 45.00% similarity) + H(+) = 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate

• Enzyme class 3: Chains A, 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⁺

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: 10.1016/j.str.2013.12.014

Structure 22:452-465 (2014)

PubMed id: 24607143

Crystal structure of vaccinia virus mRNA capping enzyme provides insights into the mechanism and evolution of the capping apparatus.

O.J.Kyrieleis, J.Chang, M.de la Peña, S.Shuman, S.Cusack.

ABSTRACT

Vaccinia virus capping enzyme is a heterodimer of D1 (844 aa) and D12 (287 aa) polypeptides that executes all three steps in m(7)GpppRNA synthesis. The D1 subunit comprises an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module and a C-terminal guanine-N7-methyltransferase (MTase) module. The D12 subunit binds and allosterically stimulates the MTase module. Crystal structures of the complete D1⋅D12 heterodimer disclose the TPase and GTase as members of the triphosphate tunnel metalloenzyme and covalent nucleotidyltransferase superfamilies, respectively, albeit with distinctive active site features. An extensive TPase-GTase interface clamps the GTase nucleotidyltransferase and OB-fold domains in a closed conformation around GTP. Mutagenesis confirms the importance of the TPase-GTase interface for GTase activity. The D1⋅D12 structure complements and rationalizes four decades of biochemical studies of this enzyme, which was the first capping enzyme to be purified and characterized, and provides new insights into the origins of the capping systems of other large DNA viruses.