PDBsum entry 3b8h

Biosynthetic protein/transferase

PDB id: 3b8h

Contents

Protein chains

823 a.a. *

207 a.a. *

Ligands

NAD ×3

Waters ×592

* Residue conservation analysis

PDB id:

3b8h

Name:

Biosynthetic protein/transferase

Title:

Structure of the eef2-exoa(e546a)-NAD+ complex

Structure:

Elongation factor 2. Chain: a, c, e. Synonym: ef-2, translation elongation factor 2, eukaryotic elongation factor 2, eef2, ribosomal translocase. Exotoxin a. Chain: b, d, f. Fragment: catalytic domain. Synonym: NAD-dependent adp-ribosyltransferase. Engineered: yes.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Pseudomonas aeruginosa. Organism_taxid: 287. Gene: eta. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.214 R-free: 0.256

Authors:

R.Jorgensen,A.R.Merrill

Key ref:

R.Jørgensen et al. (2008). The nature and character of the transition state for the ADP-ribosyltransferase reaction. Embo Rep, 9, 802-809. PubMed id: 18583986

Date:

01-Nov-07 Release date: 17-Jun-08

Protein chains

P32324  (EF2_YEAST) -  Elongation factor 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 842 a.a.

Struc: 823 a.a.*

Protein chains

P11439  (TOXA_PSEAE) -  Exotoxin A from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 638 a.a.

Struc: 207 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, C, E: E.C.3.6.5.- - ?????
• Enzyme class 3: Chains B, D, F: E.C.2.4.2.36 - NAD(+)--diphthamide ADP-ribosyltransferase.
• Reaction: diphthamide-[translation elongation factor 2] + NAD⁺ = N-(ADP-D- ribosyl)diphthamide-[translation elongation factor 2] + nicotinamide + 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

Added reference

Embo Rep 9:802-809 (2008)

PubMed id: 18583986

The nature and character of the transition state for the ADP-ribosyltransferase reaction.

R.Jørgensen, Y.Wang, D.Visschedyk, A.R.Merrill.

ABSTRACT

Exotoxin A (ExoA) from Pseudomonas aeruginosa is an important virulence factor that belongs to a class of exotoxins that are secreted by pathogenic bacteria which cause human diseases such as cholera, diphtheria, pneumonia and whooping cough. We present the first crystal structures, to our knowledge, of ExoA in complex with elongation factor 2 (eEF2) and intact NAD(+), which indicate a direct role of two active-site loops in ExoA during the catalytic cycle. One loop moves to form a solvent cover for the active site of the enzyme and reaches towards the target residue (diphthamide) in eEF2 forming an important hydrogen bond. The NAD(+) substrate adopts a conformation remarkably different from that of the NAD(+) analogue, betaTAD, observed in previous structures, and fails to trigger any loop movements. Mutational studies of the two loops in the toxin identify several residues important for catalytic activity, in particular Glu 546 and Arg 551, clearly supporting the new complex structures. On the basis of these data, we propose a transition-state model for the toxin-catalysed reaction.