PDBsum entry 5foe

Transferase

PDB id: 5foe

Contents

Protein chains

429 a.a.

Ligands

NAG ×2

GDP ×2

EDO ×10

Waters ×531

PDB id:

5foe

Name:

Transferase

Title:

Crystal structure of thE C. Elegans protein o-fucosyltransferase 2 (cepofut2) double mutant (r298k-r299k) in complex with gdp and the human tsr1 from thrombospondin 1

Structure:

Gdp-fucose protein o-fucosyltransferase 2,thrombospondin-1. Chain: a, b. Synonym: patterning defective protein 2,peptide-o-fucosyltransferase 2,o-fuct-2. Engineered: yes. Mutation: yes

Source:

Caenorhabditis elegans, homo sapiens. Human. Organism_taxid: 6239, 9606. Gene: pad-2, k10g9.3, thbs1, tsp, tsp1. Expressed in: komagataella pastoris. Expression_system_taxid: 4922.

Resolution:

1.98Å R-factor: 0.202 R-free: 0.246

Authors:

J.Valero-Gonzalez,C.Leonhard-Melief,E.Lira-Navarrete,G.Jimenez-Oses, C.Hernandez-Ruiz,M.C.Pallares,I.Yruela,D.Vasudevan,A.Lostao, F.Corzana,H.Takeuchi,R.S.Haltiwanger,R.Hurtado-Guerrero

Key ref:

J.Valero-González et al. (2016). A proactive role of water molecules in acceptor recognition by protein O-fucosyltransferase 2. Nat Chem Biol, 12, 240-246. PubMed id: 26854667 DOI: 10.1038/nchembio.2019

Date:

19-Nov-15 Release date: 27-Jan-16

Protein chains

P07996  (TSP1_HUMAN) -  Thrombospondin-1 from Homo sapiens

Seq: 1170 a.a.

Struc: 429 a.a.*

Protein chains

Q8WR51  (OFUT2_CAEEL) -  GDP-fucose protein O-fucosyltransferase 2 from Caenorhabditis elegans

Seq: 424 a.a.

Struc: 429 a.a.*

* PDB and UniProt seqs differ at 355 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.4.1.221 - peptide-O-fucosyltransferase.
• Reaction:
  1. L-seryl-[protein] + GDP-beta-L-fucose = 3-O-(alpha-L-fucosyl)-L- seryl-[protein] + GDP + H⁺
  2. L-threonyl-[protein] + GDP-beta-L-fucose = 3-O-(alpha-L-fucosyl)-L- threonyl-[protein] + GDP + H⁺

L-seryl-[protein] + GDP-beta-L-fucose = 3-O-(alpha-L-fucosyl)-L- seryl-[protein] + GDP (Bound ligand (Het Group name = GDP) corresponds exactly) + H(+)

L-threonyl-[protein] + GDP-beta-L-fucose = 3-O-(alpha-L-fucosyl)-L- threonyl-[protein] + GDP (Bound ligand (Het Group name = GDP) corresponds exactly) + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nchembio.2019

Nat Chem Biol 12:240-246 (2016)

PubMed id: 26854667

A proactive role of water molecules in acceptor recognition by protein O-fucosyltransferase 2.

J.Valero-González, C.Leonhard-Melief, E.Lira-Navarrete, G.Jiménez-Osés, C.Hernández-Ruiz, M.C.Pallarés, I.Yruela, D.Vasudevan, A.Lostao, F.Corzana, H.Takeuchi, R.S.Haltiwanger, R.Hurtado-Guerrero.

ABSTRACT

Protein O-fucosyltransferase 2 (POFUT2) is an essential enzyme that fucosylates serine and threonine residues of folded thrombospondin type 1 repeats (TSRs). To date, the mechanism by which this enzyme recognizes very dissimilar TSRs has been unclear. By engineering a fusion protein, we report the crystal structure of Caenorhabditis elegans POFUT2 (CePOFUT2) in complex with GDP and human TSR1 that suggests an inverting mechanism for fucose transfer assisted by a catalytic base and shows that nearly half of the TSR1 is embraced by CePOFUT2. A small number of direct interactions and a large network of water molecules maintain the complex. Site-directed mutagenesis demonstrates that POFUT2 fucosylates threonine preferentially over serine and relies on folded TSRs containing the minimal consensus sequence C-X-X-S/T-C. Crystallographic and mutagenesis data, together with atomic-level simulations, uncover a binding mechanism by which POFUT2 promiscuously recognizes the structural fingerprint of poorly homologous TSRs through a dynamic network of water-mediated interactions.