PDBsum entry: 2pqg

Hydrolase

PDB-id: 2pqg

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

257 a.a. *

Waters ×134

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

2pqg

Name:

Hydrolase

Title:

Crystal structure of inactive ribosome inactivating protein from maize (b-32)

Structure:

Ribosome-inactivating protein 3. Chain: a, b. Synonym: rrna n-glycosidase, b-32 protein. Engineered: yes

Source:

Zea mays. Organism_taxid: 4577. Gene: crip3. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Chains A, B: P28522 (RIPX_MAIZE)

Seq:

Struc:

Seq:

301 a.a.

Struc:

257 a.a.*

Key:

PfamA domain

Secondary structure

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

Enzyme class:

E.C.3.2.2.22   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.

Resolution:

2.38Å

R-factor:

0.211

R-free:

0.230

Authors:

A.N.S.Mak,Y.T.Wong,J.A Young,S.S.Cha,K.H.Sze,S.W.N.Au, K.B.Wong,P.C.Shaw

Key ref:

A.N.Mak et al. (2007). Structure-function study of maize ribosome-inactivating protein: implications for the internal inactivation region and the sole glutamate in the active site.. Nucleic Acids Res, 35, 6259-6267. [PubMed id: 17855394] [DOI: 10.1093/nar/gkm687]

Date:

02-May-07

Release date:

19-Feb-08

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1093/nar/gkm687

Nucleic Acids Res 35:6259-6267 (2007)

PubMed id: 17855394

Structure-function study of maize ribosome-inactivating protein: implications for the internal inactivation region and the sole glutamate in the active site.

A.N.Mak, Y.T.Wong, Y.J.An, S.S.Cha, K.H.Sze, S.W.Au, K.B.Wong, P.C.Shaw.

ABSTRACT

Maize ribosome-inactivating protein is classified as a class III or an atypical RNA N-glycosidase. It is synthesized as an inactive precursor with a 25-amino acid internal inactivation region, which is removed in the active form. As the first structural example of this class of proteins, crystals of the precursor and the active form were diffracted to 2.4 and 2.5 A, respectively. The two proteins are similar, with main chain root mean square deviation (RMSD) of 0.519. In the precursor, the inactivation region is found on the protein surface and consists of a flexible loop followed by a long alpha-helix. This region diminished both the interaction with ribosome and cytotoxicity, but not cellular uptake. Like bacterial ribosome-inactivating proteins, maize ribosome-inactivating protein does not have a back-up glutamate in the active site, which helps the protein to retain some activity if the catalytic glutamate is mutated. The structure reveals that the active site is too small to accommodate two glutamate residues. Our structure suggests that maize ribosome-inactivating protein may represent an intermediate product in the evolution of ribosome-inactivating proteins.