PDBsum entry: 2zai

Transferase

PDB id: 2zai

Contents

Protein chains

472 a.a. *

Metals

_CL ×4

_CA ×4

Waters ×34

* Residue conservation analysis

PDB id:

2zai

Name:

Transferase

Title:

Crystal structure of the soluble domain of stt3 from p. Furi

Structure:

Oligosaccharyl transferase stt3 subunit related p chain: a, b, c, d. Fragment: soluble domain, unp residues 471-967. Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 186497. Strain: dsm 3638. Gene: pf0156. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.70Å R-factor: 0.227 R-free: 0.273

Authors:

N.Maita

Key ref:

M.Igura et al. (2008). Structure-guided identification of a new catalytic motif of oligosaccharyltransferase. EMBO J, 27, 234-243. PubMed id: 18046457 DOI: 10.1038/sj.emboj.7601940

Date:

05-Oct-07 Release date: 11-Dec-07

Protein chains

Q8U4D2  (Q8U4D2_PYRFU) -  Oligosaccharyl transferase stt3 subunit related protein

Seq: 967 a.a.

Struc: 472 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (1 term)
• Biological process: protein glycosylation (1 term)
• Biochemical function: oligosaccharyl transferase activity (1 term)

DOI no: 10.1038/sj.emboj.7601940

EMBO J 27:234-243 (2008)

PubMed id: 18046457

Structure-guided identification of a new catalytic motif of oligosaccharyltransferase.

M.Igura, N.Maita, J.Kamishikiryo, M.Yamada, T.Obita, K.Maenaka, D.Kohda.

ABSTRACT

Asn-glycosylation is widespread not only in eukaryotes but also in archaea and some eubacteria. Oligosaccharyltransferase (OST) catalyzes the co-translational transfer of an oligosaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains. Here, we report that a thermophilic archaeon, Pyrococcus furiosus OST is composed of the STT3 protein alone, and catalyzes the transfer of a heptasaccharide, containing one hexouronate and two pentose residues, onto peptides in an Asn-X-Thr/Ser-motif-dependent manner. We also determined the 2.7-A resolution crystal structure of the C-terminal soluble domain of Pyrococcus STT3. The structure-based multiple sequence alignment revealed a new motif, DxxK, which is adjacent to the well-conserved WWDYG motif in the tertiary structure. The mutagenesis of the DK motif residues in yeast STT3 revealed the essential role of the motif in the catalytic activity. The function of this motif may be related to the binding of the pyrophosphate group of lipid-linked oligosaccharide donors through a transiently bound cation. Our structure provides the first structural insights into the formation of the oligosaccharide-asparagine bond.

Selected figure(s)

Figure 3.
Figure 3 Crystal structure of the C-terminal soluble domain of STT3. (A) Domain structure of P. furiosus STT3. TM, transmembrane domain; CC, central core domain, residues 471–600+683–725; IS, insertion domain, residues 601–682; P1, peripheral domain 1, residues 726–821; P2, peripheral domain 2, residues 822–967. The position of the WWDYG motif is indicated by an asterisk. (B) Stereoview of the overall structure of the C-terminal soluble domain of STT3 (residues 471–967). The WWDYG motif is shown in magenta. The disulfide bond between C638 and C658 is shown as yellow sticks. A bound metal cation is shown as a yellow sphere. (C) Different view from (B).

Figure 4.
Figure 4 Putative active site of oligosaccharyltransferase comprising the two conserved motifs. (A) Sequence alignment of the region containing the known WWDYG motif and the newly found DK motif. An initial alignment was obtained with the Mafft algorithm (Katoh et al, 2005) in the program Jalview, and then was edited manually. (B) Close-up view of the putative active site, with the WWDYG motif in cyan (W511, W512, D513, Y514, and G515), and the DK motif in yellow (D571 and K574). Alternative possible side-chain directions of W512 and D513 in the absence of crystal packing effects are indicated by gray arrows.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2008, 27, 234-243) copyright 2008.

Figures were selected by the author.