4MSM: AMSH-like protease sst2

Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound to ubiquitin. Determined by X-ray diffraction at 1.74 Å resolution. Released 18 Jun 2014.

Method: X-ray diffraction
Resolution: 1.74 Å
Organisms: Schizosaccharomyces pombe, Homo sapiens
Chains: 4
Atoms: 4,544
Mol. weight: 62.9 kDa
Ligands: PO4, ZN
Released: 18 Jun 2014

Explore 4MSM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4MSM contains 20 α-helices and 42 β-strands across 4 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: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	252-253	2	1
β-strand	259-260	2	1
β-strand	263-266	4	2
α-helix	269-282	14
β-strand	288-296	9	2
β-strand	299-307	9	2
β-strand	310-312	3	3
β-strand	317-319	3	3
α-helix	322-332	11
β-strand	335-342	8	2
α-helix	352-364	13
β-strand	369-374	6	2
α-helix	375-377	3
β-strand	379-385	7	2
α-helix	389-396	8
β-strand	411-413	3	2
α-helix	414-415	2
β-strand	420-423	4	2
β-strand	428-431	4	2

Chains B and D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	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	57-59	3
β-strand	66-71	6	4
β-strand	74-75	2	3

Chain C: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	252-253	2	6
β-strand	259-260	2	6
β-strand	263-266	4	7
α-helix	269-282	14
β-strand	288-296	9	7
β-strand	299-307	9	7
β-strand	310-312	3	8
β-strand	317-319	3	8
α-helix	322-331	10
β-strand	335-342	8	7
α-helix	352-364	13
β-strand	369-374	6	7
α-helix	375-377	3
β-strand	379-385	7	7
α-helix	389-396	8
β-strand	411-413	3	7
α-helix	414-415	2
β-strand	420-423	4	7
β-strand	428-431	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AMSH-like protease sst2	A, C	protein	197	Schizosaccharomyces pombe	Q9P371 (AlphaFold model)
Ubiquitin	B, D	protein	81	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4MSM_1 AMSH-like protease sst2 (chains A, C)
GPLGSMAGTFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLATCGILCGKLRQN
AFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTH
CSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPG
HVREINSKLQVVDLRVK

Sequence of entity 2 (B, D), FASTA

>4MSM_2 Ubiquitin (chains B, D)
GPLGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
ZN	Zinc ion	Zn	4

Water and common crystallization additives (EDO) are not listed.

Primary citation

Insights into the Mechanism of Deubiquitination by JAMM Deubiquitinases from Cocrystal Structures of the Enzyme with the Substrate and Product. Shrestha, R.K., Ronau, J.A., Davies, C.W. et al. Biochemistry (2014) 53:3199-3217. DOI 10.1021/bi5003162 · PubMed

Other PDB entries of the same protein (UniProt Q9P371 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JXE 1.45 Å, Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain
4K1R 1.63 Å, Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin
4ZD4 1.63 Å, Catalytic domain of Sst2 F403W mutant
4MS7 1.67 Å, Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain
4ZFR 1.72 Å, Catalytic domain of Sst2 F403A mutant bound to ubiquitin
4MSJ 1.8 Å, Crystal structure of S. pombe AMSH-like protease SST2 catalytic domain from P212121…
4MSD 1.9 Å, Crystal structure of Schizosaccharomyces pombe AMSH-like protein SST2 T319I mutant
4MSQ 1.95 Å, Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 catalytic domain…
4PQT 2.05 Å, Insights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal…
4ZD5 2.07 Å, Catalytic domain of Sst2 F403A mutant
4NQL 2.3 Å, The crystal structure of the DUB domain of AMSH orthologue, Sst2 from S. pombe, in…
4ZFT 2.3 Å, Catalytic domain of Sst2 F403W mutant bound to ubiquitin

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