5YSI: SdeA mART-C domain EE/AA NCA complex

SdeA mART-C domain EE/AA NCA complex. Determined by X-ray diffraction at 1.55 Å resolution. Released 29 Aug 2018.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Chains: 1
Atoms: 1,182
Mol. weight: 17.05 kDa
Ligands: NCA
Released: 29 Aug 2018

Explore 5YSI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YSI contains 6 α-helices and 8 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	763-768	6	1
α-helix	772-788	17
α-helix	790-796	7
α-helix	799-808	10
β-strand	819-821	3	2
β-strand	822	1	1
α-helix	825-831	7
β-strand	836-841	6	1
β-strand	848-852	5	2
β-strand	862-866	5	2
β-strand	871-883	13	1
α-helix	888	1
β-strand	889-899	11	1
α-helix	900-901	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitinating/deubiquitinating enzyme SdeA	A	protein	152	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Q5ZTK4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YSI_1 Ubiquitinating/deubiquitinating enzyme SdeA (chains A)
GSSQAKPPTRLFRGLNLSEEFTKGLIDQANAMIANTTERLFTDHSPEAFKQIKLNDLSKM
SGRTNASTTTEIKLVKETWDSNVIFEMLDPDGLLHSKQVGRHGEGTASAFSVYLPEDVAL
VPVKVTLDGKTQKGENRYVFTFVAVKSPDFTP

Ligands and cofactors

ID	Name	Formula	Copies
NCA	Nicotinamide	C6 H6 N2 O	1

Primary citation

Structural and Biochemical Study of the Mono-ADP-Ribosyltransferase Domain of SdeA, a Ubiquitylating/Deubiquitylating Enzyme from Legionella pneumophila. Kim, L., Kwon, D.H., Kim, B.H. et al. J Mol Biol (2018) 430:2843-2856. DOI 10.1016/j.jmb.2018.05.043 · PubMed

Other PDB entries of the same protein (UniProt Q5ZTK4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9R3T 1.98 Å, C-terminal domain of SdeA Legionella effector
5YSJ 2.06 Å, SdeA mART-C domain WT apo
6B7Q 2.2 Å, Crystal structure of Legionella effector protein sdeA (lpg2157) aa. 211-910
5YSK 2.4 Å, SdeA mART-C domain EE/AA apo
7MIR 2.5 Å, Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex
6WTG 2.63 Å, SdeA DUB Domain in complex with Ubiquitin
6G0C 2.8 Å, Crystal structure of SdeA catalytic core
8EFW 2.81 Å, Structure of SdeA DUB Domain disulfide crosslinked with Ubiquitin
7PPO 2.91 Å, Structure of SidJ/CaM bound to SdeA in pre-glutamylation state
7PQE 3.7 Å, Structure of SidJ/CaM bound to SdeA in post-catalysis state

Browse structure collections

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