5KYD

Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004843	molecular_function	cysteine-type deubiquitinase activity
A	0016579	biological_process	protein deubiquitination

Functional Information from PROSITE/UniProt

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
D	LYS27-ASP52

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site_id	PS00972
Number of Residues	16
Details	USP_1 Ubiquitin specific protease (USP) domain signature 1. GLknqGAtCYMNSlLQ

Chain	Residue	Details
A	GLY215-GLN230

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site_id	PS00973
Number of Residues	18
Details	USP_2 Ubiquitin specific protease (USP) domain signature 2. YiLhAVlvHsGdnhg..GHY

Chain	Residue	Details
A	TYR448-TYR465

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Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	ACT_SITE: Nucleophile => ECO:0000269|PubMed:12507430, ECO:0000269|PubMed:25944111, ECO:0000305|PubMed:11923872, ECO:0000305|PubMed:15053880, ECO:0000305|PubMed:16964248, ECO:0000305|PubMed:18716620, ECO:0000305|PubMed:21745816, ECO:0000305|PubMed:22411829

Chain	Residue	Details
A	ARG239
D	ARG72

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site_id	SWS_FT_FI2
Number of Residues	1
Details	ACT_SITE: Proton acceptor => ECO:0000305|PubMed:12507430

Chain	Residue	Details
A	PHE480

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site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291

Chain	Residue	Details
D	SER65

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site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457

Chain	Residue	Details
D	THR66

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site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742

Chain	Residue	Details
D	GLY76

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site_id	SWS_FT_FI6
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603

Chain	Residue	Details
D	LYS6

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site_id	SWS_FT_FI7
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
D	GLY76

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site_id	SWS_FT_FI8
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144

Chain	Residue	Details
D	LYS11
D	LYS48

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site_id	SWS_FT_FI9
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860

Chain	Residue	Details
D	LYS27

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site_id	SWS_FT_FI10
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127

Chain	Residue	Details
D	LYS29

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site_id	SWS_FT_FI11
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577

Chain	Residue	Details
D	LYS33

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site_id	SWS_FT_FI12
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106

Chain	Residue	Details
D	LYS63

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Catalytic Information from CSA

site_id	MCSA1
Number of Residues	4
Details	M-CSA 789

Chain	Residue	Details
A	PHE234	electrostatic stabiliser
A	ARG239	nucleofuge, nucleophile, proton acceptor, proton donor
A	PHE480	proton acceptor, proton donor
A	ASN497	electrostatic stabiliser

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