PDBsum entry 4jsy

Transferase

PDB id: 4jsy

Contents

Protein chains

171 a.a.

Ligands

GTP ×2

Metals

_MG ×2

Waters ×180

PDB id:

4jsy

Name:

Transferase

Title:

Structure of clostridium thermocellum polynucleotide kinase bound to gtp

Structure:

Metallophosphoesterase. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Clostridium thermocellum. Organism_taxid: 203119. Strain: atcc 27405 / dsm 1237. Gene: cthe_2768. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.14Å R-factor: 0.171 R-free: 0.205

Authors:

U.Das,L.K.Wang,P.Smith,S.Shuman

Key ref:

U.Das et al. (2013). Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial pnkp•hen1 RNA repair system. Biochemistry, 52, 4734-4743. PubMed id: 23721485 DOI: 10.1021/bi400412x

Date:

22-Mar-13 Release date: 28-Aug-13

Protein chains

A3DJ38  (A3DJ38_CLOTH) -  Metallophosphoesterase from Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)

Seq: 870 a.a.

Struc: 171 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.7.1.78 - polynucleotide 5'-hydroxyl-kinase.
• Reaction: a 5'-end dephospho-2'-deoxyribonucleoside-DNA + ATP = a 5'-end 5'-phospho-2'-deoxyribonucleoside-DNA + ADP + H⁺

5'-end dephospho-2'-deoxyribonucleoside-DNA + ATP (Bound ligand (Het Group name = GTP) matches with 96.88% similarity) = 5'-end 5'-phospho-2'-deoxyribonucleoside-DNA + ADP + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/bi400412x

Biochemistry 52:4734-4743 (2013)

PubMed id: 23721485

Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial pnkp•hen1 RNA repair system.

U.Das, L.K.Wang, P.Smith, S.Shuman.

ABSTRACT

Clostridium thermocellum Pnkp is the end-healing and end-sealing subunit of a bacterial RNA repair system. CthPnkp is composed of three catalytic modules: an N-terminal 5'-OH polynucleotide kinase, a central 2',3' phosphatase, and a C-terminal ligase. The crystal structure of the kinase domain bound to ATP•Mg(2+) revealed a rich network of ionic and hydrogen-bonding contacts to the α, β, and γ phosphates. By contrast, there are no enzymic contacts to the ribose and none with the adenine base other than a π-cation interaction with Arg116. Here we report that the enzyme uses ATP, GTP, CTP, UTP, or dATP as a phosphate donor for the 5'-OH kinase reaction. The enzyme also catalyzes the reverse reaction, in which a polynucleotide 5'-PO4 group is transferred to ADP, GDP, CDP, UDP, or dADP to form the corresponding NTP. We report new crystal structures of the kinase in complexes with GTP, CTP, UTP, and dATP in which the respective nucleobases are stacked on Arg116 but make no other enzymic contacts. Mutating Arg116 to alanine elicits a 10-fold increase in Km for ATP but has little effect on kcat. These findings illuminate the basis for nonspecific donor nucleotide utilization by a P-loop phosphotransferase.