PDBsum entry 4zt8

Hydrolase

PDB id: 4zt8

Contents

Protein chain

246 a.a.

Ligands

NAG

GOL ×2

CYT

Waters ×220

PDB id:

4zt8

Name:

Hydrolase

Title:

Structure of the complex of type 1 ribosome inactivating protein from momordica balsamina with a pyrimidine base, cytosine at 1.98 a resolution

Structure:

Ribosome inactivating protein. Chain: a. Ec: 3.2.2.22

Source:

Momordica balsamina. Bitter gourd. Organism_taxid: 3672

Resolution:

1.98Å R-factor: 0.180 R-free: 0.204

Authors:

S.Yamini,S.Pandey,P.Kaur,S.Sharma,T.P.Singh

Key ref:

S.Yamini et al. (2015). Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with cytosine, cytidine, and cytidine diphosphate. Biochem Biophys Rep, 4, 134-140. PubMed id: 29124196 DOI: 10.1016/j.bbrep.2015.09.006

Date:

14-May-15 Release date: 03-Jun-15

Supersedes:

4kjh

Protein chain

D9J2T9  (D9J2T9_MOMBA) -  rRNA N-glycosylase (Fragment) from Momordica balsamina

Seq: 246 a.a.

Struc: 246 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.2.22 - rRNA N-glycosylase.
• Reaction: Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.

DOI no: 10.1016/j.bbrep.2015.09.006

Biochem Biophys Rep 4:134-140 (2015)

PubMed id: 29124196

Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with cytosine, cytidine, and cytidine diphosphate.

S.Yamini, S.N.Pandey, P.Kaur, S.Sharma, T.P.Singh.

ABSTRACT

The type 1 ribosome inactivating protein from Momordica balsamina (MbRIP1) has been shown to interact with purine bases, adenine and guanine of RNA/DNA. We report here the binding and structural studies of MbRIP1 with a pyrimidine base, cytosine; cytosine containing nucleoside, cytidine; and cytosine containing nucleotide, cytidine diphosphate. All three compounds bound to MbRIP1 at the active site with dissociation constants of 10^-4 M-10^-7 M. As reported earlier, in the structure of native MbRIP1, there are 10 water molecules in the substrate binding site. Upon binding of cytosine to MbRIP1, four water molecules were dislodged from the substrate binding site while five water molecules were dislodged when cytidine bound to MbRIP1. Seven water molecules were dislocated when cytidine diphosphate bound to MbRIP1. This showed that cytidine diphosphate occupied a larger space in the substrate binding site enhancing the buried surface area thus making it a relatively better inhibitor of MbRIP1 as compared to cytosine and cytidine. The key residues involved in the recognition of cytosine, cytidine and cytidine diphosphate were Ile71, Glu85, Tyr111 and Arg163. The orientation of cytosine in the cleft is different from that of adenine or guanine indicating a notable difference in the modes of binding of purine and pyrimidine bases. Since adenine containing nucleosides/nucleotides are suitable substrates, the cytosine containing nucleosides/nucleotides may act as inhibitors.