PDBsum entry 1efb

Blood clotting

PDB id: 1efb

Contents

Protein chain

136 a.a.*

* C-alpha coords only

Theoretical model

PDB id:

1efb

Name:

Blood clotting

Title:

Staphylococcus aureus efb protein (theoretical model) predicted 3d structure for the alpha-carbon backbone by a de novo modeling procedure involving the use of the residue residue contact method.

Structure:

Efb protein. Chain: a

Source:

Staphylococcus aureus. Strain: newman. Other_details: protein isolated from supernate of staphylococcus aureus strain newman culture.

Authors:

D.Wade,M.Palma,J.-I.Flock,K.D.Berndt,J.Silberring, S.G.Galaktionov

Key ref:

B.W.Poland et al. (2000). Structural insights into the protein splicing mechanism of PI-SceI. J Biol Chem, 275, 16408-16413. PubMed id: 10828056 DOI: 10.1074/jbc.275.22.16408

Date:

03-Jan-99 Release date: 13-Jan-99

Protein chain

No UniProt id for this chain

Struc: 136 a.a.

Key reference

DOI no: 10.1074/jbc.275.22.16408

J Biol Chem 275:16408-16413 (2000)

PubMed id: 10828056

Structural insights into the protein splicing mechanism of PI-SceI.

B.W.Poland, M.Q.Xu, F.A.Quiocho.

ABSTRACT

PI-SceI is a member of a class of proteins (inteins) that excise themselves from a precursor protein and in the process ligate the flanking protein sequences (exteins). We report here the 2.1-A resolution crystal structure of a PI-SceI miniprecursor (VMA29) containing 10 N-terminal extein residues and 4 C-terminal extein residues. Mutations at the N- and C-terminal splicing junctions, blocking in vivo protein splicing, allowed the miniprecursor to be purified and crystallized. The structure reveals both the N- and C-terminal scissile peptide bonds to be in distorted trans conformations (tau approximately 100 degrees ). Modeling of the wild-type PI-SceI based on the VMA29 structure indicates a large conformational change (movement of >9 A) must occur to allow transesterification to be completed. A zinc atom was discovered at the C-terminal splicing junction. Residues Cys(455), His(453), and Glu(80) along with a water molecule (Wat(53)) chelate the zinc atom. The crystal structure of VMA29 has captured the intein in its pre-spliced state.

Selected figure(s)

Figure 1.
Fig. 1. a, schematic diagram of the chemical mechanism for protein splicing. The four-step reaction couples the excision of the intein (red) from the precursor protein with the ligation of the two exteins (blue and blue-green) via a native peptide bond. b, diagram of the new motif structure of PI-SceI according to Pietrokovski (9). Blocks N1-N4 and C1 and C2 (blue) contain residues involved in protein splicing; blocks EN1-EN4 (black) contain residues associated with the endonuclease/linker domain. Nucleophilic residues are highlighted below the block diagram (yellow letters in purple box), and highly conserved residues are shown in red. c, sequence alignment of the wild-type PI-SceI (VMA) and mutant miniprecursor ( VMA29). The red dash and arrow illustrate the N- and C-terminal splicing sites. Red residues in the VMA29 sequence indicate mutations made to the wild-type sequence (blue). Cys1 and Asn454 were mutated to Ala in order to block in vivo protein splicing.

Figure 3.
Fig. 3. Close-up view of the zinc coordination at the C-terminal splicing junction of molecule B of VMA29. Zinc atom is the purple sphere.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 16408-16413) copyright 2000.

Figures were selected by an automated process.