7LM3: Thr316Ala mutant of JAMM domain of S. pombe

Crystal Structure of Thr316Ala mutant of JAMM domain of S. pombe. Determined by X-ray diffraction at 2.7 Å resolution. Released 30 Jun 2021.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Chains: 2
Atoms: 2,826
Mol. weight: 44.35 kDa
Ligands: ZN, PO4
Released: 30 Jun 2021

Explore 7LM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LM3 contains 11 α-helices and 26 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: 5 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	269-276	8
α-helix	278-281	4
β-strand	288-296	9	2
β-strand	299-307	9	2
β-strand	310	1	3
β-strand	319	1	3
α-helix	322-331	10
β-strand	335-342	8	2
α-helix	352-364	13
β-strand	369-374	6	2
β-strand	379-385	7	2
α-helix	389-396	8
β-strand	411-413	3	2
β-strand	420-423	4	2
β-strand	428-431	4	2

Chain B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	252-253	2	4
β-strand	259-260	2	4
β-strand	263-266	4	5
α-helix	268-276	9
α-helix	278-282	5
β-strand	288-296	9	5
β-strand	299-307	9	5
β-strand	312	1	6
β-strand	317	1	6
α-helix	322-331	10
β-strand	335-342	8	5
α-helix	352-364	13
β-strand	369-374	6	5
β-strand	379-385	7	5
α-helix	389-396	8
β-strand	411-413	3	5
α-helix	414-415	2
β-strand	420-423	4	5
β-strand	428-431	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AMSH-like protease sst2	A, B	protein	197	Schizosaccharomyces pombe (strain 972 / ATCC 24843)	Q9P371 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7LM3_1 AMSH-like protease sst2 (chains A, B)
GPLGSMAGTFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQN
AFFITHLVIPLQEATSDACGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTH
CSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPG
HVREINSKLQVVDLRVK

Ligands and cofactors

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

Primary citation

Crystal structure of the Thr316Ala mutant of a yeast JAMM deubiquitinase: implication of active-site loop dynamics in catalysis. Shrestha, R., Das, C. Acta Crystallogr F Struct Biol Commun (2021) 77:163-170. DOI 10.1107/S2053230X21005124 · 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
4MSM 1.74 Å, Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant…
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…

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