7E9S | pdb_00007e9s

Archaeal oligosaccharyltransferase AglB from Archaeoglobus fulgidus in complex with an inhibitory peptide and a dolichol-phosphate

PDB DOI: https://doi.org/10.2210/pdb7E9S/pdb

Classification: TRANSFERASE
Organism(s): Archaeoglobus fulgidus DSM 4304, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-03-05 Released: 2021-09-08
Deposition Author(s): Taguchi, Y., Hirata, K., Kohda, D.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.252 (Depositor), 0.251 (DCC)
R-Value Work:
0.215 (Depositor), 0.216 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The structure of an archaeal oligosaccharyltransferase provides insight into the strict exclusion of proline from the N-glycosylation sequon.

Taguchi, Y., Yamasaki, T., Ishikawa, M., Kawasaki, Y., Yukimura, R., Mitani, M., Hirata, K., Kohda, D.

(2021) Commun Biol 4: 941-941

PubMed: 34354228 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-021-02473-8
Primary Citation Related Structures:
7E9S

PubMed Abstract:
Oligosaccharyltransferase (OST) catalyzes oligosaccharide transfer to the Asn residue in the N-glycosylation sequon, Asn-X-Ser/Thr, where Pro is strictly excluded at position X. Considering the unique structural properties of proline, this exclusion may not be surprising, but the structural basis for the rejection of Pro residues should be explained explicitly. Here we determined the crystal structure of an archaeal OST in a complex with a sequon-containing peptide and dolichol-phosphate to a 2.7 Å resolution. The sequon part in the peptide forms two inter-chain hydrogen bonds with a conserved amino acid motif, TIXE. We confirmed the essential role of the TIXE motif and the adjacent regions by extensive alanine-scanning of the external loop 5. A Ramachandran plot revealed that the ring structure of the Pro side chain is incompatible with the ϕ backbone dihedral angle around -150° in the rigid sequon-TIXE structure. The present structure clearly provides the structural basis for the exclusion of Pro residues from the N-glycosylation sequon.

Organizational Affiliation

Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.

Macromolecule Content

Total Structure Weight: 102.94 kDa
Atom Count: 7,233
Modeled Residue Count: 876
Deposited Residue Count: 885
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-phosphooligosaccharide-protein glycotransferase 3	A	875	Archaeoglobus fulgidus DSM 4304	Mutation(s): 1 Gene Names: aglB3, AF_0380 EC: 2.4.99.21 Membrane Entity: Yes
UniProt
Find proteins for O29867 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29867 Go to UniProtKB: O29867
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O29867
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
a polypeptide linked to an inhibitory N-glycosylation sequon-containing peptide	B	10	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J06 (Subject of Investigation/LOI) Query on J06 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	[(3S,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34Z,39S,43S)-3,7,11,15,19,23,27,31,35,39,43,47-dodecamethyloctatetraconta-6,10,14,18,22,26,30,34-octaenyl] dihydrogen phosphate C₆₀ H₁₀₇ O₄ P XTTHNPQIJYVHIB-WHVVPYAWSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
7E8 Query on 7E8 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], L [auth A], M [auth A]	(2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE C₁₇ H₃₂ O₄ LVBAGTJIDOCNIJ-XITLMJRVSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]