6WTG: SdeA DUB Domain

SdeA DUB Domain in complex with Ubiquitin. Determined by X-ray diffraction at 2.63 Å resolution. Released 3 Mar 2021.

Method: X-ray diffraction
Resolution: 2.63 Å
Organisms: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513), Homo sapiens
Chains: 2
Atoms: 1,885
Mol. weight: 29.52 kDa
Released: 3 Mar 2021

Explore 6WTG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WTG contains 13 α-helices and 18 β-strands across 2 chains. 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: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	1
α-helix	12-21	10
β-strand	30-33	4	2
β-strand	36-38	3	2
α-helix	41-47	7
β-strand	49-56	8	2
β-strand	57	1	3
β-strand	60	1	3
β-strand	62-63	2	1
β-strand	64-70	7	2
β-strand	75-79	5	2
α-helix	84-95	12
α-helix	99	1
β-strand	103-106	4	2
α-helix	109-110	2
α-helix	118-133	16
α-helix	138-140	3
α-helix	141-157	17
α-helix	160-173	14

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	5
α-helix	56-59	4
β-strand	66-71	6	4
β-strand	74-75	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitinating/deubiquitinating enzyme SdeA	A	protein	193	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)	Q5ZTK4 (AlphaFold model)
Ubiquitin	D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6WTG_1 Ubiquitinating/deubiquitinating enzyme SdeA (chains A)
MPKYVEGVELTQEGMHAIFARMGYGDITSGSIYNGVPTIDTGALNRQGFMPVLTGVGPHR
DSGHWIMLIKGPGNQYYLFDPLGKTSGEGYQNILAAQLPMGSTLSVIPNGSGLNMGLAGY
WVASAGLRAHQALNQHNPPTLLNVGQTITNEMRNELDHDGYRKITGWLRAVADEFPEGDP
QLDGKALRENTEK

Sequence of entity 2 (D), FASTA

>6WTG_2 Ubiquitin (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Insights into Ubiquitin Product Release in Hydrolysis Catalyzed by the Bacterial Deubiquitinase SdeA. Sheedlo, M.J., Kenny, S., Podkorytov, I.S. et al. Biochemistry (2021) 60:584-596. DOI 10.1021/acs.biochem.0c00760 · PubMed

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

5YSI 1.55 Å, SdeA mART-C domain EE/AA NCA complex
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
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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