PDBsum entry: 1m2t

Ribosome inhibitor, hydrolase

PDB id: 1m2t

Contents

Protein chains

248 a.a. *

262 a.a. *

Ligands

NAG ×6

FUC ×2

ADE

GOL ×8

Waters ×503

* Residue conservation analysis

PDB id:

1m2t

Name:

Ribosome inhibitor, hydrolase

Title:

Mistletoe lectin i from viscum album in complex with adenine monophosphate. Crystal structure at 1.9 a resolution

Structure:

Mistletoe lectin i a chain. Chain: a. Synonym: beta-galactoside specific lectin i a chain. Mla. M rrna n-glycosidase. Mistletoe lectin i b chain. Chain: b. Synonym: lectin chain a isoform 1

Source:

Viscum album. European mistletoe. Organism_taxid: 3972. Organ: leaf. Organ: leaf

Biol. unit:

Dimer (from PQS)

Resolution:

1.89Å R-factor: 0.210 R-free: 0.240

Authors:

R.Krauspenhaar,W.Rypniewski,N.Kalkura,K.Moore,L.Delucas,S.St A.Mikhailov,W.Voelter,C.Betzel

Key ref:

R.Krauspenhaar et al. (2002). Crystallisation under microgravity of mistletoe lectin I from Viscum album with adenine monophosphate and the crystal structure at 1.9 A resolution. Acta Crystallogr D Biol Crystallogr, 58, 1704-1707. PubMed id: 12351890 DOI: 10.1107/S0907444902014270

Date:

25-Jun-02 Release date: 24-Jun-03

Protein chain

P81446  (ML1_VISAL) -  Beta-galactoside-specific lectin 1

Seq: 564 a.a.

Struc: 248 a.a.*

Protein chain

P81446  (ML1_VISAL) -  Beta-galactoside-specific lectin 1

Seq: 564 a.a.

Struc: 262 a.a.*

* PDB and UniProt seqs differ at 50 residue positions (black crosses)

Enzyme reactions

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

 Gene Ontology (GO) functional annotation 

• Biological process: negative regulation of translation (1 term)
• Biochemical function: rRNA N-glycosylase activity (1 term)

DOI no: 10.1107/S0907444902014270

Acta Crystallogr D Biol Crystallogr 58:1704-1707 (2002)

PubMed id: 12351890

Crystallisation under microgravity of mistletoe lectin I from Viscum album with adenine monophosphate and the crystal structure at 1.9 A resolution.

R.Krauspenhaar, W.Rypniewski, N.Kalkura, K.Moore, L.DeLucas, S.Stoeva, A.Mikhailov, W.Voelter, C.h.Betzel.

ABSTRACT

The crystal structure of the ribosome-inactivating protein (RIP) mistletoe lectin I (ML-I) from Viscum album in complex with adenine has been refined to 1.9 A resolution. High quality crystals of the ML-I complex were obtained by the method of vapour diffusion using the high density protein crystal growth system (HDPCG) on the international space station, mission ISS 6A. Hexagonal crystals were grown during three months under microgravity conditions. Diffraction data to 1.9A were collected applying synchrotron radiation and cryo- techniques. The structure was refined subsequently to analyse the structure of ML-I and particularly the active site conformation, complexed by adenine that mimics the RNA substrate binding.

Selected figure(s)

Figure 1.
Figure 1 Cartoon plot of ML­I. The three domains of the A­chain are labeled I, II & III and coloured orange, green and turquoise. The helices of the secondary structure are labeled with capital letters, b­sheets in lowercase. For the B­ chain the domains I and II are coloured according to their subdomains: The linker region l1 and l2 are shown in orange, the homologous subdomains a, b, g are numbered in ascending order and coloured yellow, green and blue. The disulphide bond connecting the two chains is shown as dashed line. Dashed red circles indicate the active site region AZ at the A chain and the galactose­binding sites G1 and G2 in the B chain. The N and C terminus are indicated with N and "C".

Figure 3.
Figure 3 Stereo view of the active site of ML­I in native conformation as well in complex with adenine. Native ML­I is shown in yellow and with bound adenine in blue. Hydrogen bonds and water molecules are coloured according to the residues. The catalytic key residues for the N­glycosidase activity are: Tyr76A, Tyr115A, Glu177A and Arg168A.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1704-1707) copyright 2002.

Figures were selected by an automated process.